Browse
Submit Data
Databases
API
Help

Dataset Information

27 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The first complete chloroplast genome of Adiantum nelumboides (Pteridaceae), a rare and endangered fern species.

ABSTRACT: The complete chloroplast genome of a rare and endangered fern species Adiantum nelumboides was sequenced. The genome has a typical quadripartite structure with a length of 149,956 bp and 42.8% GC content. We annotated totally 131 genes, including 87 protein genes, 36 tRNA, and 8 rRNAs. This work provides crucial information for its phylogenetic and conservation of a critically endangered fern and its value as an ornamental and medicinal plant resource.

SUBMITTER: Liu H

PROVIDER: S-EPMC7748427 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The first complete chloroplast genome of Pteris vittata (Pteridaceae), an arsenic hyperaccumulating fern.

Project description:It is the first report on complete chloroplast genome of Pteris vittata, an arsenic hyperaccumulating fern. Its genome size is 154,130?bp, with a typical circular structure including a large single-copy (LSC) (82,623?bp) and a small single-copy (SSC) (20,957?bp) regions separated by a pair of inverted repeats (25,275?bp each). The plastome encodes 132 genes, including 87 protein-coding genes, 35 tRNA genes, eight rRNA genes, and two pseudogenes. The overall Guanine+Cytosine (GC) content is 41.7% and GC content in the IR regions is higher than in the LSC and SSC regions. Maximum likelihood (ML) tree indicated that P. vittata was clustered with Ceratopteris richardii.

| S-EPMC7799616 | biostudies-literature

The first complete chloroplast genome of Drynaria acuminata (Polypodiaceae), a local rare fern species.

Project description:The complete chloroplast genome of a local rare fern species Drynaria acuminata was sequenced. The genome has a length of 151,591 bp with 40.8% GC content, with in total 131 genes were annotated, including 88 protein genes, 35 tRNAs, and 8 rRNAs. This work provides basic information for its phylogeographical and conservation research.

| S-EPMC7850416 | biostudies-literature

The complete chloroplast genome sequence of the water fern Ceratopteris thalictroides (Pteridaceae).

Project description:This work determined and analyzed the complete chloroplast genome sequence of Ceratopteris thalictroides (Linnaeus) Brongniart 1822 (Pteridaceae). The results indicate that the total chloroplast genome size of C. thalictroides is 149,399 bp in length, and the genome contains a large single-copy (LSC) region of 83,580 bp, a small single-copy (SSC) region of 21,241 bp, and a pair of inverted repeat (IR) regions of 22,289 bp. The GC content of C. thalictroides is 36.7%. The genome encodes a total of 131 unique genes, including 82 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. The phylogenetic analysis results strongly suggest that C. thalictroides is closely related to C. cornuta.

| S-EPMC9635469 | biostudies-literature

The chloroplast genome of Adiantum reniforme var. sinense, an endangered fern endemic to China.

Project description:Adiantum reniforme var. sinense, a rare and endangered fern endemic to Chongqing, China, has been listed as one of the National Key Protected Wild Plants (Class I) in China. Here we assembled its chloroplast genome (cp genome) using Illumina sequencing reads to offer a genetic resource for future conservation genetic studies. The complete cp genome of A. reniforme var. sinense was 150,109 bp in length with an overall GC content of 42.85%. It contains a large single copy (LSC) region of 83,274 bp and a small single copy (SSC) region of 21,459 bp, separated by a pair of inverted repeat regions (IRs) of 22,688 bp each. The cp genome contains 84 protein coding genes, 28 tRNA genes, four rRNA genes, and one pseudogene (ψrps16). Phylogenetic analysis showed that A. reniforme var. sinense clustered together with four other Adiantum species and was sister to A. capillus-veneris.

| S-EPMC7782870 | biostudies-literature

The complete chloroplast genome of Platycerium wallichii (Polypodiaceae), an endangered and ornamental fern species.

Project description:The complete chloroplast genome of a staghorn fern species (Platycerium wallichii) was sequenced. The total genome was 158,286 bp in length, containing four regions: large single-copy (LSC) region (79,087 bp), small single-copy (SSC) region (21,397 bp), and two inverted repeat regions (IRs; 28,901 bp per each). In total 129 genes were annotated including 88 coding genes, 33 tRNAs, and 8 rRNAs. The overall GC content of the genome is 40.5%. Phylogenetic analysis supported the monophyly of both the subfamily Platycerioideae and the genus Platycerium. The genome data provides crucial information to support the future conservation and horticulture research.

| S-EPMC8276651 | biostudies-literature

Sporangium Exposure and Spore Release in the Peruvian Maidenhair Fern (Adiantum peruvianum, Pteridaceae).

Project description:We investigated the different processes involved in spore liberation in the polypod fern Adiantum peruvianum (Pteridaceae). Sporangia are being produced on the undersides of so-called false indusia, which are situated at the abaxial surface of the pinnule margins, and become exposed by a desiccation-induced movement of these pinnule flaps. The complex folding kinematics and functional morphology of false indusia are being described, and we discuss scenarios of movement initiation and passive hydraulic actuation of these structures. High-speed cinematography allowed for analyses of fast sporangium motion and for tracking ejected spores. Separation and liberation of spores from the sporangia are induced by relaxation of the annulus (the 'throwing arm' of the sporangium catapult) and conservation of momentum generated during this process, which leads to sporangium bouncing. The ultra-lightweight spores travel through air with a maximum velocity of ~5 m s(-1), and a launch acceleration of ~6300 g is measured. In some cases, the whole sporangium, or parts of it, together with contained spores break away from the false indusium and are shed as a whole. Also, spores can stick together and form spore clumps. Both findings are discussed in the context of wind dispersal.

| S-EPMC4596474 | biostudies-literature

The first complete chloroplast genome sequence of Paris polyphylla var. emeiensis, a rare and endangered species.

Project description:Paris polyphylla var. emeiensis H. X. Yin, H. Zhang & D. Xue is a member of the genus Paris endemic to southwest of China. The complete chloroplast (cp) genome of P. polyphylla var. emeiensis was 164,854 bp in length with 36.96% overall GC content, including a large single-copy (LSC) region of 84,438 bp and a small single-copy (SSC) region of 12,892 bp, which were separated by a pair of inverted repeats (IRs) of 33,762 bp. There were 135 genes in total, including 89 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Phylogenetic analysis indicated P. polyphylla var. emeiensis was closely related to P. fargesii and P. cronquistii.

| S-EPMC7510578 | biostudies-literature

The complete chloroplast genome of Cibotium barometz (Cibotiaceae), an endangered CITES medicinal fern.

Project description:The complete chloroplast (cp) genome sequence of Cibotium barometz, an endangered CITES medicinal fern, was determined by Illumina sequencing. Its genome is a circular molecule of 166,027 bp in length, including a pair of inverted repeats (IRs) of 29,158 bp, a large single-copy (LSC) region of 85,665 bp, and a small single-copy (SSC) region of 22,046 bp. The genome encodes 118 unique genes, involving 84 protein-coding genes, 28 tRNA genes, four rRNA genes, and two pseudogenes. Maximum likelihood tree showed that C. barometz was closely related to Alsophila spinulosa. This investigation lays solid foundations for endangered medicinal resource conservation and fern phylogenetic studies.

| S-EPMC7800266 | biostudies-literature

Complete chloroplast genome sequence of Hopea chinensis (Dipterocarpaceae), a rare and critically endangered species.

Project description:Hopea chinensis (Dipterocarpaceae) is a rare and critically endangered species. Here, we first report and characterize its complete chloroplast genome sequence based on Illumina paired-end sequencing data. The complete plastid genome was 152,054 bp, which contained inverted repeats (IR) of 21,702 bp separated by a large single-copy (LSC) and a small single-copy (SSC) of 20,462 bp and 88,188 bp, respectively. The cpDNA contains 129 genes, comprising 83 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. The overall GC content of the plastome is 37.4%. The phylogenetic analysis of 18 selected chloroplast genomes demonstrated that H. chinensis was close to the species Parashorea macrophylla.

| S-EPMC7707529 | biostudies-literature

The first complete chloroplast genome of the fern genus Polystichum (Dryopteridaceae).

Project description:The first chloroplast genome of the fern genus Polystichum Roth (Dryopteridaceae) is reported here. Polystichum deltodon (Baker) Diels belongs to subgenus Haplopolystichum (Polystichum; Dryopteridaceae), many species of which are endangered or critically endangered species. The complete chloroplast genome of P. deltodon was determined for the first time in this work, which is revealed a circle quadripartite structure of 154,143 bp in length comprising a large single-copy region (LSC) of 86,990 bp, a small single-copy region (SSC) of 21,593 bp and a pair of inverted regions (IRs) of 22,780 bp, respectively. Based on the reported chloroplast genomes of Dryopteridaceae, phylogenetic analyses suggested that P. deltodon was located nearly to the genus Crytomium, which is in agreement with previous systematic research.

| S-EPMC7748761 | 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