Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Chloroplast genome structure and phylogenetic position of Ruppia sinensis Shuo Yu & den Hartog.

ABSTRACT: Ruppia is widely distributed in marine and inland saline habitats in temperate and tropical regions. In this study, the complete chloroplast genome sequence of R. sinensis was successfully obtained using Illumina sequencing. The full length of the chloroplast genome length was 158,897?bp with a typical quadripartite structure: one large single copy (LSC) region (88,952?bp), one small single copy (SSC) region (19,047?bp), and a pair of inverted repeats (IR) (25,449?bp each). The GC content of this genome was 35.9%. The whole genome contained 136 genes, including 88 protein-coding genes, 40 tRNA genes, and eight rRNA genes. Phylogenetic analysis indicated that R. sinensis formed a distinct clade, being separated from Zostera marina and Potamogeton perfoliatus.

SUBMITTER: Yu S

PROVIDER: S-EPMC7706659 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Chloroplast genome structure and phylogenetic position of Ruppia sinensis Shuo Yu & den Hartog.

Yu Shuo S Shi Miao-Miao MM Jiang Kai K

Mitochondrial DNA. Part B, Resources 20190905 2

Ruppia is widely distributed in marine and inland saline habitats in temperate and tropical regions. In this study, the complete chloroplast genome sequence of R. sinensis was successfully obtained using Illumina sequencing. The full length of the chloroplast genome length was 158,897 bp with a typical quadripartite structure: one large single copy (LSC) region (88,952 bp), one small single copy (SSC) region (19,047 bp), and a pair of inverted repeats (IR) (25,449 bp each). The GC ...[more]

PMID: 33365790

Similar Datasets

The complete plastid genome of Ruppia brevipedunculata Shuo Yu & den Hartog.

Project description:The taxonomy of Ruppia has long been confused due to its high plasticity in morphology. In this study, the complete plastid genome sequence of Ruppia brevipedunculata was successfully sequenced by the technology of Illumina. The whole plastid genome length was 158,943 bp and contained a typical quadripartite structure including one large single copy (LSC) region (88,857 bp), one small single copy (SSC) region (19,130bp) and a pair of inverted repeats (IR) regions (25,478bp). The GC content of this genome was 35.8%. The whole genome contained 132 genes including 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The phylogenetic analysis indicated that R. brevipedunculata and R. sinensis formed a distinct clade separated from Potamogeton perfoliatus.

| S-EPMC7748422 | biostudies-literature

Chloroplast genome structure and phylogenetic position of Lophatherum gracile.

Project description:Lophatherum gracile is distributed in south China, Japan and South Asia, and it is wild in the valley, stream, woodland, forest edge and gully edge. In this study, the complete chloroplast genome sequence of Lophatherum gracile was successfully obtained using Illumina sequencing. The full length of the chloroplast genome length was 137,749 bp with a typical quadripartite structure: one large single copy (LSC) region (80,610 bp), one small single copy (SSC) region (12,429 bp), and a pair of inverted repeats (IRs) (22,355 bp each). The GC content of this genome was 38.64%. The whole genome contained 130 genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis indicated that Lophatherum gracile was closely related to Cenchrus americanus and Cenchrus longispinus.

| S-EPMC7801094 | biostudies-literature

Chloroplast genome structure and phylogenetic position of Calanthe sylvatica (Thou.) Lindl. (Orchidaceae).

Project description:Calanthe sylvatica plays an important role in horticulture and is undergoing the pressure of population decline. In this study, its complete chloroplast genome sequence was successfully obtained by the technology of Illumina sequencing. The whole chloroplast genome length was 158,828 bp with a typical quadripartite structure: one large single copy (LSC) region (87,277 bp), one small single copy (SSC) region (18,535 bp) and a pair of inverted repeats (IR) regions (26,508 bp). The GC content of this genome was 36.7%. The genome contained 118 genes consisting of 84 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The phylogenetic analysis indicated a close relationship between C. sylvatica and Calanthe triplicata.

| S-EPMC7706738 | biostudies-literature

Characterization of the chloroplast genome and its inference on the phylogenetic position of Incarvillea sinensis Lam. (Bignoniaceae).

Project description:Incarvillea sinensis Lam. is the type of the genus Incarvillea Juss., and it is widely distributed, relative to other members of the genus. In this paper, we sequenced, assembled and annotated the chloroplast genome of Incarvillea sinensis. The complete chloroplast genome is 162,088 bps in size, with overall GC content of 39.4%. We annotated 113 unique genes in the plastome sequence, including 79 protein coding genes, 30 tRNA genes, and four rRNA genes. The phylogenetic analysis based on chloroplast genome sequences resulted in a different resolution on the relationships among subgenera from the former.

| S-EPMC7872526 | biostudies-literature

Comparative genome and phylogenetic analysis revealed the complex mitochondrial genome and phylogenetic position of Conopomorpha sinensis Bradley.

Project description:Conopomorpha sinensis Bradley is a destructive pest that causes severe economic damage to litchi and longan. Previous C. sinensis research has focused on population life tables, oviposition selectivity, pest population prediction, and control technology. However, there are few studies on its mitogenome and phylogenetic evolution. In this study, we sequenced the whole mitogenome of C. sinensis by the third-generation sequencing, and analyzed the characteristics of its mitogenome by comparative genome. The complete mitogenome of C. sinensis is a typical circular and double-stranded structure. The ENC-plot analyses revealed that natural selection could affect the information of codon bias of the protein-coding genes in the mitogenome of C. sinensis in the evolutionary process. Compared with 12 other Tineoidea species, the trnA-trnF gene cluster of tRNA in the C. sinensis mitogenome appears to have a new arrangement pattern. This new arrangement has not been found in other Tineoidea or other Lepidoptera, which needs further exploration. Meanwhile, a long AT repeated sequence was inserted between trnR and trnA, trnE and trnF, ND1 and trnS in the mitogenome of C. sinensis, and the reason for this sequence remains to be further studied. Furthermore, the results of phylogenetic analysis showed that the litchi fruit borer belonged to Gracillariidae, and Gracillariidae was monophyletic. The results will contribute to an improved understanding of the complex mitogenome and phylogeny of C. sinensis. It also will provide a molecular basis for further research on the genetic diversity and population differentiation of C. sinensis.

| S-EPMC10042987 | biostudies-literature

Complete chloroplast genome sequence of Mucuna prurien and its phylogenetic position.

Project description:Mucuna pruriens is traditional medicinal plant originated in South Africa. We characterize the complete plastid genome of M. pruriens, which is a circular-mapping molecule 152,119 bp in length. The genome has a large single-copy region (LSC) of 78,258 bp and a small single-copy region (SSC) of 18,735 bp, respectively. Additionally, the overall GC content of the chloroplast genome was 35.37%. The genome contains 138 genes, including 96 protein-coding, 38 tRNA, and four rRNA genes. The gene content and structure are conserved compared to other species in the genus Glycine. The chloroplast genome and existing data were used to infer its phylogenetic position. The results showed that M. pruriens clustered together with Glycine max and G. soja. These findings provide potential genetic markers that can aid in understanding the genetic diversity of M. pruriens.

| S-EPMC8330721 | biostudies-literature

The complete chloroplast genome of Ophiopogon bodinieri Levl. and its phylogenetic position.

Project description:Ophiopogon bodinieri Levl. is an important turfgrass and ornamental cover plants which is widely used in urban garden construction in southern China. In this study, we sequenced the complete chloroplast genome of O.bodinieri on the Illumina HiSeq Platform. The chloroplast genome is 157,078 bp in length, with a typical quadripartite structure and consisting of a pair of inverted repeat (IR) regions (26,477 bp) separated by a large single copy (LSC) region (85,374 bp) and a small single copy (SSC) region (18,750 bp). It was predicted to contain a total of 132 genes, with an overall GC content of 38.63%. Phylogenetic analysis suggested O.bodinieri is closely relatedto Goodyera velutina, Anoectochilus emeiensis and Ludisia discolor.

| S-EPMC7995887 | biostudies-literature

The complete chloroplast genome sequence of Laplacea alpestris and its phylogenetic position.

Project description:Laplacea alpestris is a member of the genus Laplacea, which distributes in Central and South America. Genetic information of L. alpestris would provide guidance for the phylogenetic position of this species. Here, we reported and characterized its complete chloroplast (cp) genome using Illumina pair-end sequencing data. The total chloroplast genome size of this species was 157,211 bp, including inverted repeats (IRs) of 26,103 bp, separated by a large single copy (LSC) and a small single copy (SSC) of 86,749 and 18,256 bp, respectively. A total of 132 genes, including 37 tRNA, 8 rRNA, and 87 protein-coding genes were identified. Phylogenetic analysis showed that L. alpestris formed a monophyletic clade with Laplacea fruticosa, and then grouped with Apterosperma oblata. The systematic position of Southeast Asian Laplacea species needs further studies.

| S-EPMC7717450 | biostudies-literature

Complete chloroplast genome of Plantago asiatica and its phylogenetic position in Plantaginaceae.

Project description:Plantago asiatica, an herbaceous perennial species of Plantaginaceae, has been used as a traditional herbal medicine plant in China. In this study, the complete chloroplast (cp) genome of P. asiatica was sequenced and assembled using genome skimming data. The cp genome was 165,045 bp in length including the large single-copy (LSC, 82,964 bp) and small single-copy (SSC, 4,633 bp) regions separated by two copies of inverted region (IR, 38,724 bp). The cp genome encoded 113 unique genes, consisting of 79 protein-coding genes, 30 tRNA genes, and four rRNA genes, additionally with 27 duplicated genes in the IR regions. Phylogenetic analysis indicated that the representative species from Plantago was monophyletic and they were divided into four subgenera. P. asiatica belongs to the subgenus Plantago and was sister to P. rigida with high bootstrap value support.

| S-EPMC9103697 | biostudies-literature

The complete chloroplast genome of Diplodiscus trichospermus and phylogenetic position of Brownlowioideae within Malvaceae.

Project description:BackgroundMalvaceae is an economically important plant family of 4,225 species in nine subfamilies. Phylogenetic relationships among the nine subfamilies have always been controversial, especially for Brownlowioideae, whose phylogenetic position remains largely unknown due to the lack of samples in previous analysis datasets. To greatly clarify the phylogenetic relationship of Malvaceae, we newly sequenced and assembled the plastome of Diplodiscus trichospermus taxonomically located in Brownlowioideae, and downloaded the allied genomes from public database to build a dataset covering all subfamily members of Malvaceae.ResultsThe annotation results showed that the plastome of Diplodiscus trichospermus has a typical quadripartite structure, comprising 112 unique genes, namely 78 protein-coding genes, 30 tRNA genes and 4 rRNA genes. The total length was 158,570 bp with 37.2% GC content. Based on the maximum likelihood method and Bayesian inference, a robust phylogenetic backbone of Malvaceae was reconstructed. The topology showed that Malvaceae was divided distinctly into two major branches which were previously recognized as Byttneriina and Malvadendrina. In the Malvadendrina clade, Malvoideae and Bombacoideae formed, as always, a close sister clade named as Malvatheca. Subfamily Helicteroideae occupied the most basal position and was followed by Sterculioideae which was sister to the alliance of Malvatheca, Brownlowioideae, Dombeyoideae, and Tilioideae. Brownlowioideae together with the clade comprising Dombeyoideae and Tilioideae formed a sister clade to Malvatheca. In addition, one specific conservation SSR and three specific palindrome sequences were observed in Brownlowioideae.ConclusionsIn this study, the phylogenetic framework of subfamilies in Malvaceae has been resolved clearly based on plastomes, which may contribute to a better understanding of the classification and plastome evolution for Malvaceae.

| S-EPMC10521492 | biostudies-literature