Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome of Cephalotaxus lanceolata (Taxaceae), a plant species with extremely small populations.

ABSTRACT: Cephalotaxus lanceolata K. M. Feng ex C. Y. Cheng W. C. Cheng and L. K. Fu (Taxaceae) is a threatened plant species and a typical plant species with extremely small populations (PSESP) with only four individuals found in Gaoligong Mountain. With the aim of providing data for future conservation efforts, we sequenced the whole chloroplast (cp) genome of C. lanceolata. The results showed that the plastid genome is 136,404 bp in size. In total, 116 unique genes were annotated, including 83 protein-coding genes, 29 tRNA genes, and 4 rRNA genes. The total GC content was 35.1%. We performed phylogenetic analyses based on 12 cp genomes of Taxaceae, and we determined that the genus Cephalotaxus forms a sister group to Taxus and Pseudotaxus.

SUBMITTER: Ge J

PROVIDER: S-EPMC7995812 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The complete chloroplast genome of Cephalotaxus lanceolata (Taxaceae), a plant species with extremely small populations.

Ge Jia J Xiong Yun Y Luo Guifen G

Mitochondrial DNA. Part B, Resources 20210319 3

Cephalotaxus lanceolata K. M. Feng ex C. Y. Cheng W. C. Cheng and L. K. Fu (Taxaceae) is a threatened plant species and a typical plant species with extremely small populations (PSESP) with only four individuals found in Gaoligong Mountain. With the aim of providing data for future conservation efforts, we sequenced the whole chloroplast (cp) genome of C. lanceolata. The results showed that the plastid genome is 136,404 bp in size. In total, 116 unique genes were annotated, includi ...[more]

PMID: 33796759

Similar Datasets

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 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

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 sequence of an conifer plant Torreya grandis (Pinales, Taxaceae).

Project description:Chinese Nutmeg Tree (Torreya grandis) is a species of conifer in Taxaceae, which has a wide range in eastern and south-eastern China. Torreya grandis, endemic to eastern and south-eastern China, is a large tree, which own important economic value. Here, we report the complete chloroplast (cp) genome sequence and the cp genomic features of T. grandis. The genome was 136,949 bp long with 117 genes comprising of 82 protein-coding genes, 31 tRNA genes, and 4 rRNA genes. Phylogenetic analysis suggested that Torreya species formed a monophyletic clade within the Taxaceae family, and T. jackii is at the base of the tree and T. grandis and T. fargesii are sister groups of the inner clade.

| S-EPMC7800087 | biostudies-literature

Wild plant species with extremely small populations require conservation and reintroduction in China.

Project description: Not available

| S-EPMC3492560 | biostudies-literature

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 Torreya parvifolia, a species with extremely small population in China.

Project description:Torreya parvifolia (Torreya, Taxaceae) is endemic in Sichuan, China. It consisted of an extremely small population with less than 100 wild individuals. In this study, the complete chloroplast genome of T. parvifolia was assembled using the Illumina data. The complete chloroplast genome of T. parvifolia is 137,106 bp in length. The genome consists of 119 genes in total, including 82 protein-coding genes (PCGs), 4 ribosomal RNA (rRNA) genes, and 33 transfer RNA (tRNA) genes. Phylogenetic analysis indicated that T. parvifolia was closely related to T. fargesii, T. nucifera, and T. fargesii var. yunnanensis with strong support.

| S-EPMC7872519 | biostudies-literature

The complete chloroplast genome sequence of Styrax zhejiangensis, a species with an extremely small population.

Project description:Styrax zhejiangensis is an endemic species to China and is only distributed in Jiande, Zhejiang Province. The species is on the verge of extinction. The chloroplast genome of S. zhejiangensis was determined from Illumina pair-end sequencing data. The sequence was 157,387 bp and consisted of one large (LSC, 87,193 bp) and one small (SSC, 18,286 bp) single-copy region region, separated by a pair of inverted repeat (IR, 25,954 bp) regions. The sequence included 116 genes, including 82 protein-coding genes, 19 rRNAs and 15 tRNAs. The overall GC content was 37.0%. A maximum likelihood phylogenetic analysis showed that Styracaceae was more closely related to Symplocaceae than to Ebenaceae.

| S-EPMC7800637 | biostudies-literature

The complete chloroplast genome sequence of Amentotaxus yunnanensis (Taxaceae).

Project description:The complete chloroplast genome sequence of Amentotaxus yunnanensis has been defined in this study. The genome is 138,604 bp in length and one of the large inverted repeats found till date. The overall GC content of the genome is 35.1%. The A. yunnanensis chloroplast genome contains 118 unique genes, including 81 protein-coding genes, 31 tRNA genes, and 4 rRNA genes. Nine protein-coding genes and 6 tRNA contain a single intron, while another species (ycf3) has a couple of introns. A neighbor-joining phylogenetic analysis suggested that A. yunnanensis is closely related to A. argotaenia and A. formosana within the Taxaceae family.

| S-EPMC7687433 | biostudies-literature

Genetic diversity and structure of Rhododendron meddianum, a plant species with extremely small populations.

Project description:Rhododendron meddianum is a critically endangered species with important ornamental value and is also a plant species with extremely small populations. In this study, we used double digest restriction-site-associated DNA sequencing (ddRAD) technology to assess the genetic diversity, genetic structure and demographic history of the three extant populations of R. meddianum. Analysis of SNPs indicated that R. meddianum populations have a high genetic diversity (π = 0.0772 ± 0.0024, H E = 0.0742 ± 0.002). Both F ST values (0.1582-0.2388) and AMOVA showed a moderate genetic differentiation among the R. meddianum populations. Meanwhile, STRUCTURE, PCoA and NJ trees indicated that the R. meddianum samples were clustered into three distinct genetic groups. Using the stairway plot, we found that R. meddianum underwent a population bottleneck about 70,000 years ago. Furthermore, demographic models of R. meddianum and its relative, Rhododendron cyanocarpum, revealed that these species diverged about 3.05 (2.21-5.03) million years ago. This divergence may have been caused by environmental changes that occurred after the late Pliocene, e.g., the Asian winter monsoon intensified, leading to a drier climate. Based on these findings, we recommend that R. meddianum be conserved through in situ, ex situ approaches and that its seeds be collected for germplasm.

| S-EPMC8720705 | biostudies-literature