Browse
Submit Data
Databases
API
Help

Dataset Information

32 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome of Cycas Szechuanensis, an extremely endangered species.

ABSTRACT: In this study, we determined the complete chloroplast genome of Cycas szechuanensis (Cycadaceae, Cycas) using the Illumina sequencing data. The genome is 162,083?bp in length, including a pair of inverted repeats (IRs) of 25,003?bp each, which are separated by a large single-copy region (LSC) and a small single-copy region (SSC) with the size of 88,970 and 23,108?bp, respectively. The genome comprises 131 encoded genes in total, including 86 protein-coding genes (82 PCG species), 8 ribosomal RNA genes (4 rRNA species), and 37 transfer RNA genes (30 tRNA species). The overall GC content of the C. szechuanensis chloroplast genome is 39.42%, while the LSC, SSC, and IRs occupy 38.70, 42.03 and 36.52%, respectively. Based on complete chloroplast genome sequences from 13 species, we reconstructed the phylogenetic relationship of the 13 species and found that C. szechuanensis is closely related to C. debaoensis.

SUBMITTER: Wang Y

PROVIDER: S-EPMC7800925 | biostudies-literature | 2018 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The complete chloroplast genome of Cycas Szechuanensis, an extremely endangered species.

Wang Yaling Y Wang Zefu Z Zhang Lei L Yang Xiaoyue X

Mitochondrial DNA. Part B, Resources 20180910 2

In this study, we determined the complete chloroplast genome of Cycas szechuanensis (Cycadaceae, Cycas) using the Illumina sequencing data. The genome is 162,083 bp in length, including a pair of inverted repeats (IRs) of 25,003 bp each, which are separated by a large single-copy region (LSC) and a small single-copy region (SSC) with the size of 88,970 and 23,108 bp, respectively. The genome comprises 131 encoded genes in total, including 86 protein-coding genes (82 PCG species), 8 ...[more]

PMID: 33474385

Similar Datasets

The complete chloroplast genome of Cycas bifida, an extremely small population protected species.

Project description:Cycas bifida (Dyer) K.D.Hill (2004) is an extremely small population-protected species of China. In this study, we reported the first chloroplast genome sequence of C. bifida. The chloroplast genome of C. bifida included two single-copy regions (large single-copy (LSC) and small single-copy (SSC)) and a pair of inverted repeats (IRs) regions comprising 88,946 bp, 23,107 bp, and 25,053 bp, respectively. The complete chloroplast genome of C. bifida contains 131 genes, including 86 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. The overall GC content of the C. bifida chloroplast genome is 39.41%, and the LSC, SSC, and IR regions occupy 38.70%, 36.52%, and 42.02%, respectively. A phylogenetic analysis was performed based on complete chloroplast genomes from 15 species and found that C. bifida was closely related to Cycas szechuanensis W.C.Cheng & L.K.Fu.

| S-EPMC8451596 | biostudies-literature

The complete chloroplast genome of Horsfieldia hainanensis, an Endangered species with extremely small populations.

Project description:Horsfieldia hainanensis is an Endangered species with extremely small populations, inhabiting the dense forest in ravines. It has high development and utilization value in the seed oil, fatty acids, volatile oils, and liposoluble constituent. In this study, the complete chloroplast genome of Horsfieldia hainanensis was sequenced. It is 155,774 bp in size with a typical quadripartite structure: a large single-copy (LSC) region of 87,124 bp, a small single-copy (SSC) region of 20,612 bp, and 2 inverted repeat (IR) regions of 24,020 bp. The genome contains 117 genes, including 75 protein-coding genes, 34 tRNA genes, and 8 rRNA genes, 13 genes have one intron and 3 three genes have two introns. The overall GC contents of the chloroplast genome was 39.1%. The phylogenetic tree based 11 complete chloroplast genome sequences of Magnoliales shows that H. hainanensis is closely related to Horsfieldia pandurifolia.

| S-EPMC7706491 | biostudies-literature

Characterization of the complete chloroplast genome of Cycas ferruginea, a vulnerable species.

Project description:Cycas ferruginea F. N. Wei (1994) is recorded in the list of wild plant protection in China as a national first-class protected plant. The complete chloroplast genome of C. ferruginea was analyzed for the first time in this article. The genome is 162,045 bp in length, which contains a pair of inverted repeats (IRs) of 25,048 bp each, a large single-copy (LSC) region of 88,827 bp, and a small single-copy (SSC) region of 23,122 bp. The genome comprises a total of 130 encoded genes, including 85 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. The total GC content is 39.44%, and the corresponding values of the LSC, SSC, and IRs are 38.73%, 36.56%, and 42.02%, respectively. The phylogenetic relationships were reconstructed based on the complete chloroplast genome sequences of 16 species. Results showed that C. ferruginea is close to C. debaoensis, C. bifida, and C. szechuanensis.

| S-EPMC9225770 | biostudies-literature

Complete chloroplast genome sequences of two endangered Phoebe (Lauraceae) species.

Project description:BackgroundPhoebe (Lauraceae) comprises of evergreen trees or shrubs with approximately 100 species, distributed in tropical and subtropical Asia and Neotropical America. A total of 34 species and three varieties occur in China. Despite of economic and ecological value, only limited genomic resources are available for this genus.ResultsWe sequenced the two complete chloroplast (cp) genomes of Phoebe chekiangensis and P. bournei using Illumina sequencing technology via a combined strategy of de novo and reference-guided assembly. We also performed comparative analyses with the cp genomes of P. sheareri and P. sheareri var. oineiensis previously reported. The chloroplast genomes of P. chekiangensis and P. bournei identically contain 112 genes consisting of 78 protein coding genes, 30 tRNA genes, and 4 rRNA genes, with the size of 152,849 and 152,853 bp, respectively. From the two chloroplast genomes, 131 SSRs were identified and 12 different SSRs located in five protein coding genes. The analysis showed the extremely conserved structure of chloroplast genomes with surprisingly little variations at the LSC/IR and SSC/IR boundaries. Moreover, the mean nucleotide diversity was found to be 0.162% for 77 regions, suggesting an extraordinarily low level of sequence divergence. Four highest divergent regions (trnH-psbA, rps14-trnT, petA-psbJ, ccsA-ndhD) with the percentage of nucleotide diversity higher than 0.50% were identified, which had potential use for species identification and phylogenetic studies.ConclusionThis study will facilitate our understanding of population genetics, phylogenetic relationship and plant evolution of Phoebe species.

| S-EPMC5597560 | biostudies-literature

The complete chloroplast genome of Craigia yunnanensis, an endangered plant species with extremely small populations (PSESP) from South China.

Project description:Craigia yunnanensis is an Endangered tree species, enlisted in the national plant species with extremely small population (PSESP) of China for urgent protection. The chloroplast genome is characterized using Illumina pair-end sequencing data. The whole chloroplast genome is 163,166 bp in length and consists of a pair of inverted repeat (IR) regions of 25,573 bp each, which are separated by the large single copy (LSC: 91,580 bp) region and small single copy (SSC: 20,440 bp) regions. The chloroplast genome encodes 113 unique genes, including 79 protein-coding genes (PCGs), 30 tRNA, and 4 rRNA genes. The overall GC content of the whole chloroplast genome is 36.4%. The phylogenetic tree revealed a close relationship between C. yunnanensis and Tilia species of Malvaceae family.

| S-EPMC7706985 | biostudies-literature

The complete chloroplast genome of an endangered species Cymbidium mastersii (Orchidaceae).

Project description:Cymbidium mastersii Griff. & Lindl. is an endangered orchid. In this study, we report the complete chloroplast (cp) genome sequence and the cp genome features of C. mastersii. The cp genome sequence of C. mastersii was 155,362?bp in length. It included one large single-copy region (LSC, 84,465?bp), one small single-copy region (SSC, 20,647?bp), and two inverted repeat regions (IRs, 25,125?bp). The cp genome encoded 130 genes, of which 107 were unique genes (80 protein-coding genes, 23 tRNAs, and 4 rRNAs). The maximum-likelihood phylogenetic analysis showed that C. mastersii was a sister of C. erythraeum and C. nanulum.

| S-EPMC7706812 | biostudies-literature

The complete chloroplast genome of the endangered species Cephalotaxus hainanensis (Cephalotaxaceae).

Project description:Cephalotaxus hainanensis is an endangered tree endemic to China with high medicinal values. In this study, the complete chloroplast genome of C. hainanensis was de novo assembled using Illumina high-throughput sequencing technology. The whole chloroplast genome was 136,877?bp long with an asymmetric base composition (32.6% A, 17.6% C, 17.4% G and 32.4% T). The genome annotation predicted a total of 114 genes, including 82 protein-coding genes, 28 tRNA genes, and four rRNA genes. The neighbour-joining phylogenetic analysis based on 41 complete chloroplast genome sequences showed that C. hainanensis was more closely related to the congeneric C. sinensis. The assembled chloroplast genome of C. hainanensis will provide useful genomic data both for the phylogenetic research of Cephalotaxus and the conservation of this endangered species.

| S-EPMC7800532 | biostudies-literature

The complete chloroplast genome of Pterospermum menglunense (Sterculiaceae), an endangered species.

Project description:Pterospermum menglunense is the endangered plant species of the genus Pterospermum in the family Sterculiaceae. In the study, the complete genome was 162,421bp in length, including of two inverted repeats (IRA and IRB, 25,572 bp), separated by a large single-copy region (LSC, 90,754 bp) and a small single-copy region (SSC, 20,523 bp). The genome annotation reveals a total of 132 genes, including 37 transfer RNA (tRNA) genes, 8 ribosomal RNA (rRNA) genes, and 87 protein-coding (PCG) genes. The phylogenetic tree showed P. menglunense is closely related to Pterospermum kingtungense.

| S-EPMC8008881 | biostudies-literature

The complete chloroplast genome of an Endangered species Cymbidium Nanulum (Orchidaceae).

Project description:Cymbidium nanulum Y.S.Wu & S.C.Chen is an IUCN Red listed Endangered species and distributes in South-Central China and Hainan. Here, we report the complete chloroplast (cp) genome sequence and the cp genome features of C. nanulum. The complete chloroplast (cp) genome sequence of C. nanulum was 149,776 bp in length. It presented a typical quadripartite structure including one large single-copy region (LSC, 85,392 bp), one small single-copy region (SSC, 14,210 bp), and two inverted repeat regions (IRs, 25,087 bp). The cp genome encoded 133 genes, of which 104 were unique genes (77 protein-coding genes, 23 tRNAs, and 4 rRNAs). The maximum-likelihood phylogenetic analysis showed that C. nanulum was closely related to other species of genus Cymbidium.

| S-EPMC7687592 | biostudies-literature

The complete chloroplast genome of Pterospermum kingtungense, a Critically Endangered species.

Project description:Pterospermum kingtungense (Pterospermum, Sterculiaceae) is a Critically Endangered species. In this study, we reported a complete chloroplast genome of P. kingtungense based on high-throughput sequencing data. The size of chloroplast genome was 162,929 bp, including a large single-copy region (LSC: 91,535 bp) and a small single-copy region (SSC: 20,464 bp), separated by a pair of inverted repeats (IRa and IRb: 25,465 bp). The genome encoded 126 genes in total, including 81 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. The overall GC content of the P. kingtungense chloroplast genome is 36.39%. The phylogenetic tree showed P. kingtungense clustered together with the family Sterculiaceae.

| S-EPMC7801019 | biostudies-literature