Browse
Submit Data
Databases
API
Help

Dataset Information

25 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

SUBMITTER: Lee SC

PROVIDER: S-EPMC7871828 | biostudies-literature | 2016 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

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

Lee Sang-Choon SC Kim Kyunghee K Hwang Yoon-Jung YJ Lim Ki-Byung KB Yang Tae-Jin TJ

Mitochondrial DNA. Part B, Resources 20160419 1

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 i ...[more]

PMID: 33644375

Similar Datasets

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 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 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 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 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

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

The Complete Chloroplast Genomes of Three Cardiocrinum (Liliaceae) Species: Comparative Genomic and Phylogenetic Analyses.

Project description:The genus Cardiocrinum (Endlicher) Lindley (Liliaceae) comprises three herbaceous perennial species that are distributed in East Asian temperate-deciduous forests. Although all three Cardiocrinum species have horticultural and medical uses, studies related to species identification and molecular phylogenetic analysis of this genus have not been reported. Here, we report the complete chloroplast (cp) sequences of each Cardiocrinum species using Illumina paired-end sequencing technology. The cp genomes of C. giganteum, C. cathayanum, and C. cordatum were found to be 152,653, 152,415, and 152,410 bp in length, respectively, including a pair of inverted repeat (IR) regions (26,364-26,500 bp) separated by a large single-copy (LSC) region (82,186-82,368 bp) and a small single-copy (SSC) region (17,309-17,344 bp). Each cp genome contained the same 112 unique genes consisting of 30 transfer RNA genes, 4 ribosomal RNA genes, and 78 protein-coding genes. Gene content, gene order, AT content, and IR/SC boundary structures were almost the same among the three Cardiocrinum cp genomes, yet their lengths varied due to contraction/expansion of the IR/SC borders. Simple sequence repeat (SSR) analysis further indicated the richest SSRs in these cp genomes to be A/T mononucleotides. A total of 45, 57, and 45 repeats were identified in C. giganteum, C. cathayanum, and C. cordatum, respectively. Six cpDNA markers (rps19, rpoC2-rpoC1, trnS-psbZ, trnM-atpE, psaC-ndhE, ycf15-ycf1) with the percentage of variable sites higher than 0.95% were identified. Phylogenomic analyses of the complete cp genomes and 74 protein-coding genes strongly supported the monophyly of Cardiocrinum and a sister relationship between C. cathayanum and C. cordatum. The availability of these cp genomes provides valuable genetic information for further population genetics and phylogeography studies on Cardiocrinum.

| S-EPMC5222849 | biostudies-literature

The complete plastome sequence of Lilium wahingtonianum Kellogg (Liliaceae).

Project description:Lilium washingtonianum Kellogg is native to Western America and grows on slope in high subalpine. In the present study, the complete plastome of L. washingtonianum was sequenced. The plastome sequence was 151,967?bp long, with a large single copy region of 81,393?bp, a small single copy region of 17,352?bp, and two inverted repeat regions of 26,611?bp each. Total 133 genes were identified, including 83 coding genes, 8 ribosomal RNAs, 38 transfer RNAs, and 4 pseudogenes. Among four pseudogenes, pseudo ndhF gene was the first to report among Lilium species so far. The phylogenetic position of L. washingtonianum was sister to L. superbum but American lilies were not monophyletic.

| S-EPMC7800384 | biostudies-literature