Browse
Submit Data
Databases
API
Help

Dataset Information

42 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome sequence of the mangrove associate species Talipariti tiliaceum.

ABSTRACT: Talipariti tiliaceum is an evergreen mangrove associate species distributed throughout the world. In this study, the complete chloroplast genome sequence of T. tiliaceum was assembled and characterized using high-throughput sequencing data. The chloroplast genome was found to be 161 766 bp in length, consisting of large single-copy (LSC) and small single-copy (SSC) regions of 89 273 and 19 551 bp, respectively, which were separated by a pair of 26 471 bp inverted repeat (IR) regions. The genome contained 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. A phylogenetic tree including 66 chloroplast genomes from various species revealed that T. tiliaceum was most related to T. hamabo of the same genus.

SUBMITTER: Qiu Z

PROVIDER: S-EPMC8284133 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The complete chloroplast genome sequence of the mangrove associate species Talipariti tiliaceum.

Qiu Zhimin Z Zhu Yunxiao Y Du Zhaokui Z Bao Pingyong P

Mitochondrial DNA. Part B, Resources 20210714 8

Talipariti tiliaceum is an evergreen mangrove associate species distributed throughout the world. In this study, the complete chloroplast genome sequence of T. tiliaceum was assembled and characterized using high-throughput sequencing data. The chloroplast genome was found to be 161 766 bp in length, consisting of large single-copy (LSC) and small single-copy (SSC) regions of 89 273 and 19 551 bp, respectively, which were separated by a pair of 26 471 bp inverted repeat (IR) region ...[more]

PMID: 34345700

Similar Datasets

Complete chloroplast genome sequence of the mangrove species Kandelia obovata and comparative analyses with related species.

Project description:As one of the most cold and salt-tolerant mangrove species, Kandelia obovata is widely distributed in China. Here, we report the complete chloroplast genome sequence K. obovata (Rhizophoraceae) obtained via next-generation sequencing, compare the general features of the sampled plastomes of this species to those of other sequenced mangrove species, and perform a phylogenetic analysis based on the protein-coding genes of these plastomes. The complete chloroplast genome of K. obovata is 160,325 bp in size and has a 35.22% GC content. The genome has a typical circular quadripartite structure, with a pair of inverted repeat (IR) regions 26,670 bp in length separating a large single-copy (LSC) region (91,156 bp) and a small single-cope (SSC) region (15,829 bp). The chloroplast genome of K. obovata contains 128 unique genes, including 80 protein-coding genes, 38 tRNA genes, 8 rRNA genes and 2 pseudogenes (ycf1 in the IRA region and rpl22 in the IRB region). In addition, a simple sequence repeat (SSR) analysis found 108 SSR loci in the chloroplast genome of K. obovata, most of which are A/T rich. IR expansion and contraction regions were compared between K. obovata and five related species: two from Malpighiales and three mangrove species from different orders. The mVISTA results indicated that the genome structure, gene order and gene content are highly conserved among the analyzed species. The phylogenetic analysis using 54 common protein-coding genes from the chloroplast genome showed that the plant most closely related to K. obovata is Ceriops tagal of Rhizophoraceae. The results of this study provide useful molecular information about the evolution and molecular biology of these mangrove trees.

| S-EPMC6756139 | biostudies-literature

The complete chloroplast genome of Pluchea pteropoda Hemsl, a mangrove associate plant.

Project description:Pluchea pteropoda Hemsl is a mangrove associate plant of Asteraceae with medicinal properties such as anti-inflammation and fever-relieving. Here, our study presented the complete chloroplast (cp) genome of Pluchea pteropoda Hemsl. The cp genome of P. pteropoda was 152,300 bp in length, including a large single copy (LSC) region of 84,127 bp, a small single copy (SSC) region of 18,093 bp and a pair of inverted repeats (IR) regions of 25,040 bp. A total of 111 unique genes were found, comprising 79 protein-coding genes, 28 tRNA genes, and 4 rRNA genes. The GC content of the cp genome was 37.5%. Phylogenetic analysis suggested that P. pteropoda nested in Pluchea clade, which was closely related to Ageratina adenophora and Senecio scandens. The work provides beneficial data for following researches on the genetic variation, species delimitation, phylogeny and classification of Pluchea genus.

| S-EPMC8158197 | biostudies-literature

Illumina sequencing of complete chloroplast genome of Avicennia marina, a pioneer mangrove species.

Project description:Mangrove tree Avicenna marina has great ecological significance in maintaining coastal ecosystem, but its unique potential for gene functions and genetic diversity underlying ecological adaptation remains investigation. In this study, the chloroplast genome of A. marina was first characterized by sequencing chloroplast DNA with Illumina technology. The A. marina genome was 147,909 bp in size with a typical quadripartite structure, which was deposited in GenBank under the accession number MT108381.

| S-EPMC7510616 | biostudies-literature

Complete chloroplast genome sequence of a major invasive species, crofton weed (Ageratina adenophora).

Project description:BACKGROUND:Crofton weed (Ageratina adenophora) is one of the most hazardous invasive plant species, which causes serious economic losses and environmental damages worldwide. However, the sequence resource and genome information of A. adenophora are rather limited, making phylogenetic identification and evolutionary studies very difficult. Here, we report the complete sequence of the A. adenophora chloroplast (cp) genome based on Illumina sequencing. METHODOLOGY/PRINCIPAL FINDINGS:The A. adenophora cp genome is 150, 689 bp in length including a small single-copy (SSC) region of 18, 358 bp and a large single-copy (LSC) region of 84, 815 bp separated by a pair of inverted repeats (IRs) of 23, 755 bp. The genome contains 130 unique genes and 18 duplicated in the IR regions, with the gene content and organization similar to other Asteraceae cp genomes. Comparative analysis identified five DNA regions (ndhD-ccsA, psbI-trnS, ndhF-ycf1, ndhI-ndhG and atpA-trnR) containing parsimony-informative characters higher than 2%, which may be potential informative markers for barcoding and phylogenetic analysis. Repeat structure, codon usage and contraction of the IR were also investigated to reveal the pattern of evolution. Phylogenetic analysis demonstrated a sister relationship between A. adenophora and Guizotia abyssinica and supported a monophyly of the Asterales. CONCLUSION:We have assembled and analyzed the chloroplast genome of A. adenophora in this study, which was the first sequenced plastome in the Eupatorieae tribe. The complete chloroplast genome information is useful for plant phylogenetic and evolutionary studies within this invasive species and also within the Asteraceae family.

| S-EPMC3350484 | biostudies-literature

The complete chloroplast genome sequence of Chrysophyllum cainito, a semidomesticated species.

Project description:Chrysophyllum cainito is a semi-domesticated species widely cultivated in tropical regions, such as the Americas and Southeast Asia. In Yunnan, Guangdong, and Fujian Provinces, China, C. cainito is planted as an edible tropical fruit that was introduced from Southeast Asia. In this study, the chloroplast genome sequence of C. cainito was assembled and characterized using Illumina sequencing. The whole chloroplast genome of C. cainito is 158,841 bp long and consists of four regions: a large single-copy region (LSC, 88,256 bp), two inverted repeat regions (IRs, 25,958 bp), and a small single copy (SSC, 18,669 bp) region. The composition of the four bases in the circular chloroplast genome is 31.20% A, 32.00% T, 18.02% G, and 18.78% C, and the GC content of the entire C. cainito chloroplast genome is 36.8%. A total of 129 genes were annotated in the C. cainito chloroplast genome, of which 84 were protein-coding genes, 37 were transfer RNA (tRNA) genes, and eight were ribosomal RNA (rRNA) genes. The phylogenetic analysis indicated that C. cainito was most closely related to Pouteria campechiana. This study provides a foundation for further investigation of chloroplast genome evolution and genetic variation within semi-domesticated species.

| S-EPMC7510614 | biostudies-literature

Complete chloroplast genome sequence of Adenophora racemosa (Campanulaceae): Comparative analysis with congeneric species.

Project description:Adenophora racemosa, belonging to the Campanulaceae, is an important species because it is endemic to Korea. The goal of this study was to assemble and annotate the chloroplast genome of A. racemosa and compare it with published chloroplast genomes of congeneric species. The chloroplast genome was reconstructed using de novo assembly of paired-end reads generated by the Illumina MiSeq platform. The chloroplast genome size of A. racemosa was 169,344 bp. In total, 112 unique genes (78 protein-coding genes, 30 tRNAs, and 4 rRNAs) were identified. A Maximum likelihood (ML) tree based on 76 protein-coding genes divided the five Adenophora species into two clades, showing that A. racemosa is more closely related to Adenophora stricta than to Adenophora divaricata. The gene order and contents of the LSC region of A. racemosa were identical to those of A. divaricata and A. stricta, but the structure of the SSC and IRs was unique due to IR contraction. Nucleotide diversity (Pi) >0.05 was found in eleven regions among the three Adenophora species not included in sect. Remotiflorae and in six regions between two species (A. racemosa and A. stricta).

| S-EPMC7971521 | biostudies-literature

Interspecific variation and phylogenetic relationship between mangrove and non-mangrove species of a same family (Meliaceae)-insights from comparative analysis of complete chloroplast genome.

Project description:The mahogany family, Meliaceae, contains 58 genera with only one mangrove genus: Xylocarpus. Two of the three species of the genus Xylocarpus are true mangroves (X. granatum and X. moluccensis), and one is a non-mangrove (X. rumphii). In order to resolve the phylogenetic relationship between the mangrove and non-mangrove species, we sequenced chloroplast genomes of these Xylocarpus species along with two non-mangrove species of the Meliaceae family (Carapa guianensis and Swietenia macrophylla) and compared the genome features and variations across the five species. The five Meliaceae species shared 130 genes (85 protein-coding genes, 37 tRNA, and eight rRNA) with identical direction and order, with a few variations in genes and intergenic spacers. The repetitive sequences identified in the rpl22 gene region only occurred in Xylocarpus, while the repetitive sequences in accD were found in X. moluccensis and X. rumphii. The TrnH-GUG and rpl32 gene regions and four non-coding gene regions showed high variabilities between X. granatum and the two non-mangrove species (S. macrophylla and C. guianensis). In addition, among the Xylocarpus species, only two genes (accD and clpP) showed positive selection. Carapa guianensis and S. macrophylla owned unique RNA editing sites. The above genes played an important role in acclimation to different stress factors like heat, low temperature, high UV light, and high salinity. Phylogenetic analysis with 22 species in the order Sapindales supported previous studies, which revealed that the non-mangrove species X. rumphii is closer to X. moluccensis than X. granatum. Overall, our results provided important insights into the variation of genetic structure and adaptation mechanism at interspecific (three Xylocarpus species) and intergeneric (mangrove and non-mangrove genera) levels.

| S-EPMC10309054 | biostudies-literature

Complete chloroplast genome sequence of Heritiera angustata (Malvaceae): an endangered plant species.

Project description:Heritiera angustata (Malvaceae) is an evergreen tree distributed in the Chinese provinces of Hainan and Yunnan and in Cambodia. In China, it is listed as 'Endangered' (EN) China Red List of Higher Plants, although it is not protected by law. The complete chloroplast (cp) genome sequence of this threatened species is reported in this study, based on high-throughput sequencing (Illumina). The complete cp genome is 168, 953?bp in length, containing a pair of inverted repeat regions (IRs) of 34,491?bp, a large single copy (LSC) region of 89,054?bp, and a small single copy (SSC) region of 10,917?bp. The cp genome contains 129 genes, consisting of 85 protein-coding genes, 36 tRNA genes and eight rRNA genes. The overall AT content in the cp genome of H. angustata is 63.2%. The phylogenetic analyses indicate that there is a close relationship between H. angustata and Firmiana pulcherrima.

| S-EPMC7800114 | biostudies-literature

Characterization of the complete chloroplast genome sequence of Dalbergia species and its phylogenetic implications.

Project description:The pantropical plant genus Dalbergia comprises approximately 250 species, most of which have a high economic and ecological value. However, these species are among the most threatened due to illegal logging and the timber trade. To enforce protective legislation and ensure effective conservation of Dalbergia species, the identity of wood being traded must be accurately validated. For the rapid and accurate identification of Dalbergia species and assessment of phylogenetic relationships, it would be highly desirable to develop more effective DNA barcodes for these species. In this study, we sequenced and compared the chloroplast genomes of nine species of Dalbergia. We found that these chloroplast genomes were conserved with respect to genome size, structure, and gene content and showed low sequence divergence. We identified eight mutation hotspots, namely, six intergenic spacer regions (trnL-trnT, atpA-trnG, rps16-accD, petG-psaJ, ndhF-trnL, and ndhG-ndhI) and two coding regions (ycf1a and ycf1b), as candidate DNA barcodes for Dalbergia. Phylogenetic analyses based on whole chloroplast genome data provided the best resolution of Dalbergia, and phylogenetic analysis of the Fabaceae showed that Dalbergia was sister to Arachis. Based on comparison of chloroplast genomes, we identified a set of highly variable markers that can be developed as specific DNA barcodes.

| S-EPMC6938520 | biostudies-literature

The complete chloroplast genome sequence of Gynostemma yixingense and comparative analysis with congeneric species.

Project description:Gynostemma yixingense, an important medicinal member of the Cucurbitaceae family, is an endemic herbaceous species distributed in East China. It is morphologically similar to the plants in the same genus, which resulted in some confusion in identification and application. Meanwhile, there are still some controversies in taxonomy. Herein, the complete chloroplast genome sequence of G. yixingense was obtained by Illumina paired-end sequencing technology and compared to other chloroplast genome sequences of congeneric species. The complete chloroplast genome of G. yixingense is 157,910 bp in length with 36.94% GC content and contains a large single-copy (LSC) region of 86,791 bp, a small single-copy (SSC) region of 18,635 bp and a pair of inverted repeat (IR) regions of 26,242 bp. The whole genome contains 133 unique genes, including 87 protein-coding genes, 37 tRNA genes, eight rRNA genes and one pseudogene. In addition, 74 simple sequence repeats (SSRs) were identified, most of which were A/T rich. The phylogenetic analysis indicated that G. yixingense had the closest relationship to G. laxiflorum. The result of this study provided an important theoretical basis for chloroplast genome and phylogenetic analysis of G. yixingense.

| S-EPMC7521087 | biostudies-literature