Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterization of the chloroplast genome of a rare species in China, Lilium martagon var. pilosiusculum.

ABSTRACT: Lilium martagon var. pilosiusculum is an endangered species with high ornamental value in Xinjiang province (China). In this study, we reported a complete chloroplast genome of L. martagon var. pilosiusculum, which was de novo assembled using the next-generation sequencing data. The complete chloroplast genome is 152,816 in length, including a large single copy region of 82,265?bp and a small single copy region of 17,541?bp and two inverted repeat regions of 26,505?bp. A total of 110 functional genes were encoded, consisting of 76 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. The overall AT content of the chloroplast genome is 63.00%. In addition, 68 SSRs and 31 large repeat sequences were found. In the maximum likelihood tree, a strong phylogenetic signal showed that L. martagon var. pilosiusculum is a species of lilium.

SUBMITTER: Zhou Y

PROVIDER: S-EPMC7800655 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Characterization of the chloroplast genome of a rare species in China, Lilium martagon var. pilosiusculum.

Zhou Yanping Y Bi Yu Y Yan Qiheng Q Jia Guixia G Du Yunpeng Y

Mitochondrial DNA. Part B, Resources 20180401 1

Lilium martagon var. pilosiusculum is an endangered species with high ornamental value in Xinjiang province (China). In this study, we reported a complete chloroplast genome of L. martagon var. pilosiusculum, which was de novo assembled using the next-generation sequencing data. The complete chloroplast genome is 152,816 in length, including a large single copy region of 82,265 bp and a small single copy region of 17,541 bp and two inverted repeat regions of 26 ...[more]

PMID: 33474193

Similar Datasets

The complete chloroplast genome of a rare species in Korea, Lilium Dauricum Ker Gawl.

Project description:Lilium dauricum Ker Gawler is a wild lily species that belongs to section Sinomartagon and is one of the ancestors of the Asiatic hybrid lilies. Unique traits such as disease resistance and early flowering make L. dauricum a desirable resource for interspecific hybridization. However, in Korea, the natural resources of L. dauricum are being exhausted by excessive exploitation and require urgent conservation. In this study, the complete chloroplast genome of L. dauricum was generated using Illumina paired-end sequencing technology, and its structure was compared with that of other Lilium species. The chloroplast genome was 152,063 bp long, with a typical quadripartite structure including a pair of inverted repeat regions (26,492 bp) separated by a large (81,485 bp) and small (17,584 bp) single-copy (SC) region. The genome encodes 131 different genes, including 85 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. A phylogenetic analysis strongly supported the relationship of L. dauricum with other members of Sinomartagon and Martagon lilies.

| S-EPMC7707306 | biostudies-literature

The complete chloroplast genome sequence of Lilium concolor var. pulchellum.

Project description:Lilium concolor var. pulchellum is a perennial herbaceous plant with high ornamental and edible value; it is a critical breeding parent of Asiatic hybrids. In this study, we reported the complete chloroplast genome of L. concolor var. pulchellum. The total size of the genome is 152,126 bp with a GC content of 37.0%. It has a conserved quadripartite structure comprising 136 genes, including 38 tRNA genes, 8 rRNA genes, 83 protein-coding genes, and 7 pseudogenes. Phylogenetic analysis strongly supported a close relation between L. concolor var. pulchellum and L. callosum. The complete plastome sequence of L. concolor var. pulchellum could provide useful information for phyletic evolution of the genus Lilium.

| S-EPMC9487941 | biostudies-literature

Characterization of the chloroplast genome of a rare species Polygonatum sp. in China (Asparagaceae, Asparagales).

Project description:Polygonatum (Asparagaceae) is a medicinal and food plant that is naturally distributed in most of countries throughout the temperate Northern Hemisphere. Here we report on the complete chloroplast (cp) genome sequence of a rare species Polygonatum sp. without defoliation in late autumn or winter. The cp genome is 157,696 bp in size and includes two inverted repeat regions of 52,821bp, which is separated by a large single-copy region of 84,359 bp and a small single copy region of 20,516 bp. A total of 132 genes were predicted, including 38 tRNA, 8 rRNA, and 86 protein-coding genes. Phylogenetic analysis placed Polygonatum sp. under the subfamily Nolinoideae of the family Asparagaceae.

| S-EPMC7748811 | 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 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 speciosum Var. gloriosoides, an important breeding parent.

Project description:Lilium speciosum var. gloriosoides is an important breeding parent with high ornamental and edible value in worldwide. In this study, we reported a complete chloroplast genome of L. speciosum var. gloriosoides, which was de novo assembled using the next-generation sequencing data. The whole genome is 152,912 bp in length and includes one large single copy (LSC) region of 70,693 bp, one small single copy (SSC) region of 17,517 bp, and a pair of inverted repeat (IR) region of 26,539 bp. A total of 131 functional genes were encoded, consisting of 76 protein-coding genes, 36 transfer RNA genes, and eight ribosomal RNA genes. The overall AT content of the chloroplast genome is 63.00%. In the maximum likelihood, a strong phylogenetic signal showed that L. speciosum var. gloriosoides is a species of Lilium, which is the first major genome in section Archelirion.

| S-EPMC7720947 | 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 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

Characterization of the complete chloroplast genome sequence of Daphne retusa Hemsl. (Thymelaeaceae), a rare alpine plant species in northwestern China.

Project description:Daphne retusa Hemsl. (Thymelaeaceae) is an evergreen shrub plant. First, we characterized the complete nucleotide sequence of chloroplast (cp) genome of D. retusa. The total length of cp genome was found to be 170,553 bp, including a large single copy (LSC) region of 84,886 bp, a small single copy (SSC) region of 2,437 bp, and a pair of inverted repeats (IRs) of 41,617 bp. The cp genome of Daphne retusa Hemsl. contains 134 genes, including 90 protein-coding genes (75 PCG species), 37 transfer RNA genes (29 tRNA species), and 6 rRNA genes (3 RNA species). A total of 13 genes (trnK-UUU, trnS-CGA, atpF, rpoC1, trnL-UAA, trnC-ACA, petD, rpl16, rpl2, ndhB, trnE-UUC, ndhA, and trnA-UGC) contain a single intron, and one gene (ycf3) contains two introns. The GC content in whole cp genome, LSC region, SSC region, and IR region was 36.75%, 34.83%, 28.19%, and 38.96% respectively, like other Thymelaeaceae plants. Phylogenetic analysis suggested that D. retusa has a close relationship with congeneric Daphne tangutica.

| S-EPMC8245106 | biostudies-literature

Complete chloroplast genome sequence of Heteroplexis incana (Asteraceae), a rare species endemic to China.

Project description:Heteroplexis incana (Asteraceae) is a rare species endemic to China. Here, we report and characterize the complete chloroplast genome sequence of H. incana based on Illumina paired-end sequencing data. The complete plastid genome was 152,605 bp in length, which contained two inverted repeats (IRs) of 24,954 bp separated by a large single-copy (LSC) and a small single copy (SSC) of 84,427 bp and 18,270 bp, respectively. The cpDNA contains 132 genes, comprising 85 protein-coding genes, 37 tRNA genes, 8 rRNA genes. The overall GC content of the plastome is 37.3%. The phylogenetic analysis of 17 selected chloroplast genomes demonstrated that Heteroplexis incana was closely related to Aster indicus.

| S-EPMC7706452 | biostudies-literature