Browse
Submit Data
Databases
API
Help

Dataset Information

15 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome of Lilium nepalense (Liliaceae).

ABSTRACT: 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.

SUBMITTER: Wu H

PROVIDER: S-EPMC7889093 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

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

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 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

The complete chloroplast genomes of Lilium tsingtauense Gilg (Liliaceae).

Project description:Lilium tsingtauense, known as 'Korean wheel lily' and 'Twilight lily', is a lily species naturally distributed in Korea. The complete chloroplast genome sequences of L. tsingtauense was obtained by de novo assembly using whole-genome next-generation sequencing data. The chloroplast genome of L. tsingtauense was 152,710?bp in length and consisted of four distinct regions, such as large single-copy region (82,059?bp), small single-copy region (17,619?bp) and a pair of inverted repeat regions (26,516?bp). The genome contained a total of 113 genes, including 79 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Phylogenetic analysis with the reported chloroplast genomes revealed that L. tsingtauense is most closely related to Lilium hansonii, a lily species native to Korea.

| S-EPMC7871828 | biostudies-literature

The complete chloroplast genome of Lilium brownii F.E.Brown var. viridulum Baker (Liliaceae).

Project description:Lilium brownii F.E.Brown var. viridulum Baker is a medicinal and food plant that is widely distributed in northern and eastern Asia. Here, we report on the complete chloroplast genome sequence of L. brownii var. viridulum. The chloroplast genome is 152,665 bp in size and includes two inverted repeat regions of 53,052 bp, which is separated by a large single-copy region of 82,085 bp and a small single-copy region of 17,528 bp. A total of 131 genes were predicted, including 38 tRNA, 8 rRNA, and 85 protein-coding genes. Phylogenetic analysis placed L. brownii var. viridulum under the family Liliaceae.

| S-EPMC7748718 | biostudies-literature

The complete chloroplast genome of Yishui Lily 140 (Liliaceae Lilium lancifolium) yielded by next-generation sequencing

Project description:Abstract Yishui Lily 140 (Lilium lancifolium) is a hybrid lily species which was bred from wild lily varieties due to its edible and medicinal value. In this study, we have sequenced the complete chloroplast (cp) of L. lancifolium. The complete cp sequence is 152,643 bp long, with a large single copy (LSC) region of 82,084 bp, a small single copy (SSC) region of 17,513 bp, and two inverted repeat (IR) regions of 26,492 bp each. The GC contents of the complete cp genomes are 37.0%. It contains 132 genes, including 86 coding genes, 8 ribosomal RNAs, and 38 transfer RNAs. Among them, 16 different genes have a single intron and the remaining two genes have double introns, including nine cis-splicing and one trans-splicing genes. Compared with other species, we found three high variation hot spots and 96 repeats sequence. The genetic information of Lilium can be enriched as well as identifying proximal species. They are edible and have medicinal value for humans. Therefore, sequencing of Yishui Lily 140 is important to explore the cp genome composition.

| S-EPMC8567886 | biostudies-literature

Characteristics and phylogenetic analysis of the complete chloroplast genome of Lilium concolor Salisb. (Liliaceae) from Jilin, China.

Project description:Lilium concolor Salisb. is a perennial herb with high ornamental and medicinal value in China. The complete chloroplast genome sequence of L. concolor was assembled using high-throughput sequencing data. The chloroplast genome of L. concolor is 152,625 bp in length and consists of large single-copy (82,056 bp) and small single-copy (17,585 bp) regions, and a pair of inverted repeat (26,492 bp) regions. A total of 131 genes were annotated, these included 85 protein-coding, 38 tRNA, and eight rRNA genes, with an overall GC content of 37.0%. Phylogenetic analysis with 48 chloroplast genomes fully resolved L. concolor in a clade with L. amabile, L. callosum, and L. pumilum. This study further confirmed that chloroplast genomes in the genus Lilium are highly conserved, which supports the conclusions from previous reports.

| S-EPMC8667917 | biostudies-literature

Complete chloroplast genome of Tulipa buhseana (Liliaceae).

Project description: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.

| S-EPMC7782963 | biostudies-literature

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 plastome sequence of Lilium Bulbiferum (Liliaceae).

Project description:The flower shape of Lilium bulbiferum L. is different from that of the other European lilies. The phylogenetic position of the plant has been changed frequently. In the present study, we have sequenced the complete plastome of L. bulbiferum. The plastome sequence was 152,686?bp long, with a large single copy (LSC) region of 82,083?bp, a small single copy (SSC) region of 17,619?bp, and two inverted repeat (IR) regions of 26,492?bp each. It contained 133 genes, including 83 coding genes, 8 ribosomal RNAs, 38 transfer RNAs, and 4 pseudogenes. The GC contents of LSC, SSC, and IT were 34.8%, 30.7%, and 42.5%, respectively, corresponding to 37.0% of the total GC content. The phylogenetic position of L. bulbiferum was closely related to the north-eastern lilies.

| S-EPMC7800588 | 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