Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterization of the complete chloroplast genome of endangered Cycads Zamia fischeri Miq. ex Lem.

ABSTRACT: The whole chloroplast (cp) genome sequence of Zamia fischeri has been characterized. The cp genome length was 164,767 bp in length, with a GC content of 39.7%, containing a large single copy (LSC) of 90,226 bp, a small single copy (SSC) of 23,223 bp, and a pair of inverted repeats (IRs) of 25,659 bp. The genome contained 127 genes, including 88 protein-coding genes, 31 tRNA genes, and 8 rRNA genes. A phylogenetic analysis based on complete chloroplast genomes in Cycads indicates that Z. fischeri clustered with another Zamia (Z. furfuracea). This complete chloroplast sequence offers a promising tool for further species identification, population genetic conservation, and evolutionary studies of Zamiaceae, as well as for Cycadales.

SUBMITTER: Lei JY

PROVIDER: S-EPMC7800899 | biostudies-literature | 2018 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Characterization of the complete chloroplast genome of endangered Cycads Zamia fischeri Miq. ex Lem.

Lei Jin-Yan JY Hinsinger Damien Daniel DD Jiang Guo-Feng GF

Mitochondrial DNA. Part B, Resources 20181026 2

The whole chloroplast (cp) genome sequence of Zamia fischeri has been characterized. The cp genome length was 164,767 bp in length, with a GC content of 39.7%, containing a large single copy (LSC) of 90,226 bp, a small single copy (SSC) of 23,223 bp, and a pair of inverted repeats (IRs) of 25,659 bp. The genome contained 127 genes, including 88 protein-coding genes, 31 tRNA genes, and 8 rRNA genes. A phylogenetic analysis based on complete chloroplast genomes in Cycads indicates that Z ...[more]

PMID: 33474414

Similar Datasets

Complete chloroplast genome and phylogenetic analysis of Meliosma oldhamii Miq. ex Maxim. (Sabiaceae).

Project description:Meliosma oldhamii Miq. is a deciduous arbor and a member of Sabiaceae. It is one of the rare and protected plants with outstanding ornamental and economic value in Jiangsu, China. In addition to the resource values indicated above, there are numerous other elements that require additional research, including the chloroplast (cp) genomic information. In this work, the complete cp genome sequence of M. oldhamii was assembled and characterized for the first time. The complete cp genome of M. oldhamii was 159,950 base pair (bp) in length, including a large single-copy (LSC) region of 87,147 bp, a small single-copy (SSC) region of 18,015 bp, and the inverted repeats (IRs) region of 27,394 bp. It contains 131 genes, including 37 tRNA genes, eight rRNA genes, 85 protein-coding genes, and one pseudogene. The overall GC content of M. oldhamii cp genome was 37.95%. The placement of M. oldhamii in the phylogenetic tree constructed using the complete cp genome is largely congruent with previous studies. The clustering of Meliosma is non-monophyletic, aligns more closely with existing morphological taxonomic studies, thereby enhancing the scholarly and scientific nature of this research.

| S-EPMC10769540 | biostudies-literature

Complete chloroplast genome of Gypsophila oldhamiana Miq. (Caryophyllales: Caryophyllaceae).

Project description:The complete chloroplast genome sequence of Gypsophila oldhamiana Miq., a species of the Caryophyllaceae family, was assembled and analyzed from the de novo assembly of Illumina paired-end sequencing data. The total length of the chloroplast genome of G. oldhamiana was 152,675 bp including a large single-copy (LSC) region of 83,552 bp, a small single-copy (SSC) region of 17,349 bp, and a pair of identical inverted repeat regions (IRs) of 25,887 bp. The genome possessed a total of 130 genes, including 85 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. The phylogenetic analysis of G. oldhamiana with 14 related species discovered the closest taxonomical relationship with Gypsophila vaccaria voucher in the Caryophyllaceae family.

| S-EPMC8583823 | biostudies-literature

The complete chloroplast genome of Orthosiphon aristatus (Blume) Miq. (Lamiaceae).

Project description:Orthosiphon aristatus (Blume) Miq. 1858 is a Lamiaceae plant. It is mainly found in southern China. It is an excellent medicinal plant. The complete chloroplast genome of O. aristatus is 152,155 bp in length, with an average depth of 287×, and the GC content was 37.86%, a large single-copy (LSC) region of 83,098 bp, a small single-copy (SSC) region of 17,665 bp, and an inverted repeats (IRs) region of 25,696 bp make up the genome's typical tetragonal shape. In addition, the genome consisted of 128 genes, including 85 protein-coding genes, 35 transfer RNA (tRNA), and eight ribosomal RNA (rRNA) genes. A monophyletic group was established by O. aristatus and 13 plants from five genera of Lamiaceae, according to the phylogenetic tree. In contrast, an isolated monophyletic group was formed by the alien plant Cinnamomum aromaticum. The ML tree bootstrap value was relatively high, and O. aristatus was most closely related to Ocimum tenuiflorum and Ocimum basilicum. This study can help with species identification and phylogenetic analysis within O. aristatus and Lamiaceae species.

| S-EPMC10786424 | biostudies-literature

Complete chloroplast genome of Kadsura coccinea (Lem.) A.C.Sm. (Schisandraceae): genome structure and evolution.

Project description:Kadsura coccinea (Lem.) A.C.Sm. in the Schisandraceae family is woody vine plant, which produce edible red fruits that are rich in nutrients and antioxidant activities. Herein, we assembled the complete chloroplast genome of Kadsura coccinea by next-generation sequencing technologies. The complete chloroplast genome sequence of Kadsura coccinea is 145,413 base pairs (bp) in length, including a pair of inverted repeat regions (IRs, 16,431 bp), one large single-copy region (LSC, 94,511 bp), one small single-copy region (SSC, 18,040 bp). Besides, the complete chloroplast genome contains 126 genes in total, including 82 protein-coding genes, 35 tRNA genes, and 8 rRNA genes. Phylogenetic analysis showed that Kadsura coccinea has the closest relationship with Kadsura longipedunculata. Our study lay a foundation for further research of Kadsura coccinea.

| S-EPMC8018480 | biostudies-literature

The complete chloroplast genome of Distylium tsiangii Chun ex Walker, a rare and endangered plant.

Project description:Distylium tsiangii Chun ex Walker is an evergreen tree species endemic to China. It has been classified as critically endangered in the Red List of China Higher Plants. Here, we sequenced, assembled, and analyzed the complete chloroplast (cp) genome of D. tsiangii. The plastome is 159,125 bp in length, with a typical quadripartite structure and consisting of a pair of inverted repeat (IR) regions (26,220 bp) separated by a large single copy (LSC) region (87,897 bp) and a small single copy (SSC) region (18,788 bp). The overall GC content was 38.00%. A total of 131 genes were annotated, including 37 tRNA genes, 86 protein-coding genes, and eight rRNA genes. Phylogenetic analysis showed that D. tsiangii was more closely related to Parrotia subaequalis.

| S-EPMC7748841 | biostudies-literature

The complete chloroplast genome of Hylotelephium erythrostictum (Miq.) H. Ohba (Crassulaceae).

Project description:The species Hylotelephium erythrostictum is well known as an ornamental plant in China. Here, we report the complete chloroplast genome (cp) of H. erythrostictum using the next-generation sequencing. It shows a total length of 151,707 bp with typical quadripartite structure. The genome is composed of the large single copy region (LSC) of 83,070 bp, the small single copy region (SSC) of 17,018 bp, and two separated inverted regions (IRs) of 25,793 bp, respectively. It contains 134 genes, including 80 protein-coding genes (PCGs), 8 rRNA genes, and 37 tRNA genes. The overall GC content of the cp genome is 37.7%. Maximum likelihood (ML) tree based on ten complete chloroplast genomes of Crassulaceae and one outgroup species suggested a monophyly formed by H. erythrostictum together with Hylotelephium ewersii, which demonstrate a comparably closer phylogenetic relationship. The complete chloroplast genome of this H. erythrostictum provides valuable information and further phylogenetic reconstruction of the Crassulaceae family.

| S-EPMC8843096 | biostudies-literature

Characterization of the complete chloroplast genome of a Chinese endangered species Cymbidium mannii.

Project description:Cymbidium mannii is an endangered species belonging to the first ranking in protection category in China with important ornamental value and breeding value. This study used Illumina high-throughput sequencing technologies to sequence and analyze the complete chloroplast genome of C. mannii. The genome features of C. mannii and the phylogenetic relationships among Orchidaceae species were reported and established. The complete chloroplast genome is 152,544 bp in length, consisting of a pair of inverse duplication regions 25,357 bp, a large single-copy region 86,014 bp and a small single-copy region 15,816 bp. The entire genome contains 74 mRNA genes, 30 tRNA genes and 4 rRNA genes. The phylogenetic tree of 23 Orchidaceae species revealed C. mannii is more closely related to Cymbidium aloifolium.

| S-EPMC7782536 | biostudies-literature

Characterization of the complete chloroplast genome of a Chinese Endangered species Cymbidium mastersii.

Project description:Cymbidium mastersii is an endangered species belonging to the first ranking in protection category in China with important ornamental value and breeding value. This study used Illumina high-throughput sequencing technologies for C. mastersii of chloroplast genome sequencing. The genome features of C. mastersii and the phylogenetic relationships were reported and established. The complete chloroplast genome is 156,317 bp in length, consisting of a pair of inverse duplication regions 26,544 bp, a large single-copy region 85,360 bp and a small single-copy region 17,869 bp. The entire genome contains 73 mRNA genes, 30 tRNA genes and 4 rRNA genes. The phylogenetic tree of 23 Orchidaceae species revealed C. mastersii is more closely related to Cymbidium eburneum.

| S-EPMC7971198 | biostudies-literature

The complete chloroplast genome sequence of Xylosma racemosa (Siebold & Zucc.) Miq. (Salicaceae).

Project description:Xylosma racemosa (Siebold & Zucc.) Miq. which plays an important role in ecology, medicine and economy, is a deciduous species of Salicaceae. In this paper, we sequenced, assembled, and annotated the chloroplast (cp) genome of X. racemosa (Siebold & Zucc.) Miq. by using the sequencing data from Illumina Novaseq platform. The complete cp genome of X. racemosa is 157,262 bp in length, containing a large single-copy (LSC) region of 84,289 bp, and a small single-copy (SSC) region of 17,817 bp. It contains 131 genes, including 8 rRNA genes, 37 tRNAs genes and 86 protein-coding genes. The GC content of X. racemosa cp genome is 36.74%. The phylogenetic analysis suggests that X. racemosa is a sister species to Xylosma congesta in Salicaceae.

| S-EPMC8451645 | biostudies-literature

The complete chloroplast genome of Prince Ginseng, Pseudostellaria heterophylla (Miq.) Pax (Caryophyllaceae).

Project description:We presented complete chloroplast genome of Prince Ginseng, Pseudostellaria heterophylla which is 149,795 bp long and has four subregions: 81,460 bp of large single copy (LSC) and 16,983 bp of small single copy (SSC) regions are separated by 25,676 bp of inverted repeat (IR) regions including 126 genes (81 CDS, 8 rRNAs, and 37 tRNAs). The overall GC content of the chloroplast genome is 36.5% and those in the LSC, SSC, and IR regions are 34.3%, 29.4%, and 42.3%, respectively. Phylogenetic trees of 25 Caryophyllaceae species present phylogenetic position of P. heterophylla among available Pseudostellaria species.

| S-EPMC7687451 | biostudies-literature