Browse
Submit Data
Databases
API
Help

Dataset Information

23 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Complete chloroplast genome of Tulipa buhseana (Liliaceae).

ABSTRACT: The complete chloroplast genome of Tulipa buhseana was sequenced and reported here. The circular genome of T. buhseana is 152,062 bp in length and contains 133 functional genes consisting of 87 coding sequences, 38 tRNA genes, and 8 rRNA genes. With 1 species from Smilacaceae and 1 species from Alstroemeriaceae as outgroup, phylogenetic relationships of 8 Liliaceae species based on their chloroplast genomes indicated that T. buhseana is closest to T. altaica.

SUBMITTER: Ju X

PROVIDER: S-EPMC7782963 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete chloroplast genome of Amana baohuaensis (Liliaceae).

Project description:Amana baohuaensis is a new species that was just named in 2019. Here, we obtained the complete chloroplast (cp) genome of A. baohuaensis using the Illumina paired-end sequencing technology. The cp genome has a typical quadripartite structure with 150,757 bp in length, containing a large single-copy (LSC) region of 81,757 bp, a small single-copy (SSC) region of 16,962 bp, and two inverted repeat (IR) regions of 26,019 bp. The total GC content is 36.73%, of which, the GC content of LSC, SSC and IR regions are 34.63%, 30.11% and 42.20%, respectively. The cp genome of A. baohuaensis contains 111 unique genes, including 78 protein-coding genes, 29 tRNA genes, and four rRNA genes. The Maximum Parsimony (MP) phylogenetic analysis suggested that A. baohuaensis had the closest relationship with A. wanzhensis, and all Amana species grouped together with high bootstrap support.

| S-EPMC7646578 | biostudies-literature

The complete chloroplast genome of Lilium nepalense (Liliaceae).

Project description:Lilium nepalense is a useful plant species not only for its showy flowers but also has high medicinal value. In this study, the whole chloroplast genome of L. nepalense was sequenced for the first time. The genome size of L. nepalense, was 152,956bp, with typical tetragonal structure: one large single copy (82,573 bp), one small single copy (17,527 bp), and a pair of inverted repeat regions (IRs, 26,428 bp). The overall GC content was 37.0%. The complete genome contained 131 genes, including 85 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Phylogenetic analysis showed that L. nepalense was a close relationship between L. leucanthum and L. henryi. Phylogenetic analysis placed L. nepalense under the family Liliaceae.

| S-EPMC7889093 | biostudies-literature

The complete chloroplast genome sequence of Campylandra chinensis (Liliaceae).

Project description:The complete chloroplast genome of Campylandra chinensis from China was analyzed using next-generation sequencing. The chloroplast genome was a 169,419 bp circular molecule and was predicted to contain a large single copy (LSC) of 86,752 bp and a small single copy (SSC) of 21,363 bp, which were separated by a pair of 25,340 bp inverted repeats (IRs). A total of 132 unique genes were annotated, including 86 protein coding genes, 38 tRNA genes, and 8 rRNA genes. Among these genes, 19 genes contained one or two introns. The overall GC contents of the plastid genome was 37.2%. Phylogenetic analysis showed that C. chinensis and Polygonatum species clustered to one clade with a high bootstrap value at the base of the phylogenetic tree.

| S-EPMC7800404 | biostudies-literature

Characterization of the complete chloroplast genome of Chlorophytum comosum (Liliaceae).

Project description:Chlorophytum comosum is a perennial ornamental plant in the family Liliaceae, it is also a valuable medicinal plant. To enrich the genetic resources of C. comosum, its chloroplast genome was determined by Illumina sequencing data. The chloroplast genome is a typical quadripartite structure with a size of 153,983 bp, of which the LSC region is 83,471 bp, the SSC region is 18,010 bp, and the pair of IR regions is 26,251 bp. The overall GC content is 37%. It contains 131 genes, including 85 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Phylogenetic analyses showed that C. comosum is closely related to Chlorophytum rhizopendulum. However, it can be distinguished from other plants. This study enriches the sequence resources of C. comosum and provides important data for the development of molecular identification markers.

| S-EPMC7748608 | biostudies-literature

The complete chloroplast genome of Lilium rosthornii Diels (Liliopsida: Liliaceae) from Hunan, China.

Project description:Lilium rosthornii is the perennial herbaceous bulbous plant belonging to the Lily of the Liliaceae, with high ornamental value and medicinal values. In this present study, we sequenced the complete chloroplast genome of Lilium rosthornii by Illumina Hiseq X Ten and PacBio RS technologies firstly. The genome size of L. rosthornii, was 152,242bp, with typical tetragonal structure: one large single-copy (LSC, 81,875 bp), one small single-copy (SSC, 17,553 bp), and a pair of inverted repeat regions (IRs, 26,407 bp). The overall GC content was 37.02%. The complete genome contained 131 genes, including 85 protein-coding genes, 38 tRNA genes, and eight rRNA genes. Phylogenetic analysis placed L. rosthornii under the family Liliaceae.

| S-EPMC7889155 | biostudies-literature

Characterization of the complete chloroplast genome of toad lily Tricyrtis Macropoda (Liliaceae).

Project description:Tricyrtis (Liliaceae) is an endemic genus in East Asia. Many of the species in the genus are in Endangered condition due to habitat loss and extensive horticultural usage in recent decades. In present study, we reported the first Tricyrtis chloroplast (cp) genome, Tricyrtis macropoda, based on Illumina pair-end sequencing data. The complete chloroplast genome size is 155,778?bp. In total, 131 genes were identified, including 85 protein-coding genes, 8 rRNA genes, and 38 tRNA genes. Fifteen genes are containing introns (clpP and ycf3 contained two introns) and 14 genes had two copies. The overall GC content of this genome was 37.4%. A further phylogenomic analysis of Liliales, including 62 taxa, was conducted for the placement of genus Tricyrtis. The complete plastome of T. marcropoda will provide a valuable resource for further genetic conservation, phylogenomic, and evolution studies in the genus and family.

| S-EPMC7800006 | biostudies-literature

The complete chloroplast genome sequence of Lilium tsingtauense Gilg (sect. Martagon, Liliaceae).

Project description:Lilium tsingtauense Gilg, known as Twilight Lily and distributed in Korea and eastern China, possessed a 151,983?bp chloroplast genome (cpDNA) sequence composed of a large single copy (81,424?bp), a small single copy (17,575?bp), and two inverted repeat regions (26,492?bp each). This cpDNA encoded 81 protein-coding genes, 30 tRNAs and four rRNAs. In contrast to the overlaps between ycf1 and ndhF at the IR/SSC junctions in other Lilium species, there was no record of this pattern in L. tsingtauense. Moreover, variable poly A sequences located downstream of start codon caused different annotations of cemA among Lilium species.

| S-EPMC7871846 | biostudies-literature

The complete chloroplast genome of Polygonatum odoratum (Liliaceae), an endemic medicinal herb.

Project description:In this study, we sequenced the complete chloroplast genome of Polygonatum odoratum with Illumina sequencing technology. The complete chloroplast genome length is 156,082 bp shows a typical tetrad structure, which manifests as one large and one small single copy (LSC and SSC) regions of 85,009 and 18,513 bp, isolated by two inverted repeat regions (IRs) of 26,280 bp. This study annotated altogether 131 unique genes, consisting of 86 protein-encoding genes, 8 rRNA, and 38 tRNA. According to the maximum likelihood phylogenetic tree based on eight complete chloroplast genomes, P. odoratum shows a close association with additional Maianthemum genus. The chloroplast genome-wide for P. odoratum would help to conserve the precious natural populations.

| S-EPMC7671610 | biostudies-literature

The complete chloroplast genome of Polygonatum odoratum (Liliaceae), an endemic medicinal herb.

Project description:In this study, we sequenced the complete chloroplast genome of Polygonatum odoratum with Illumina sequencing technology. The complete chloroplast genome length is 156,082bp, shows a typical tetrad structure, which manifests as one large and one small single copy (LSC and SSC) regions of 85,009 and 18,513bp, isolated by two inverted repeat regions (IRs) of 26,280bp. This study annotated altogether 131 unique genes, consisting of 86 protein-encoding genes, 8 rRNA and 38tRNA. According to the maximum likelihood phylogenetic tree based on 8 complete chloroplast genomes, P. odoratum shows close association with additional Maianthemum genus. The chloroplast genome-wide for P. odoratum would help to conserving the precious natural populations.

| S-EPMC7655049 | biostudies-literature

The complete chloroplast genome of Lilium amoenum (Liliopsida: Liliaceae) from Yunnan, China.

Project description:Lilium amoenum E. H. Wilson ex Sealy is classified in Liliaceae, and it is an important ornamental plant with wonderful rose-red color and pleasant rose fragrance. In this study, we sequenced the complete chloroplast genome of L. amoenum by Illumina Hiseq X Ten and PacBio RS technologies. The genome size of L. amoenum is 152,280 bp, and displays a typical quadripartite structure: one large single-copy (LSC, 81,977 bp), one small single-copy (SSC, 17,539 bp), and a pair of inverted repeat regions (IRs, 26,382 bp). The overall GC content was 37.0%. The complete genome contained 131 genes, including 85 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Phylogenetic analysis showed that L. amoenum is closely related to L. taliense and L. bakerianum. The present study could afford crucial genetic information for further researches on the genus and related genera.

| S-EPMC7971213 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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