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| Title |
Complete chloroplast genome of the medicinal plant Amomum compactum: gene organization, comparative analysis, and phylogenetic relationships within Zingiberales
|
|---|---|
| Published in |
Chinese Medicine, February 2018
|
| DOI | 10.1186/s13020-018-0164-2 |
| Pubmed ID | |
| Authors |
Ming-li Wu, Qing Li, Jiang Xu, Xi-wen Li |
| Abstract |
Amomum compactum is one of the basic species of the traditional herbal medicine amomi fructus rotundus, with great pharmacology effect. The system position ofA. compactumis not clear yet, and the introduction of this plant has been hindered by many plant diseases. However, the correlational molecular studies are relatively scarce. The total chloroplast (cp) DNA was extracted according to previous studies, and then sequenced by 454 GS FLX Titanium platform. Sequence assembly was complished by Newbler. Genome annotation was preformed by CPGAVAS and tRNA-SCAN. Then, general characteristics of theA. compactumcp genome and genome comparsion with three Zingiberaceae species was analyzed by corresponding softwares. Additionally, phylogenetical trees were reconstructed, based on the shared protein-coding gene sequences among 15 plant taxa by maximum parsimony (MP) and maximum likelihood (ML) methods. TheA. compactumcp genome with a classic quadripartite structure, consisting of a pair of reverse complement repeat regions (IRa/IRb) of 29,824 bp, a large single copy (LSC, 88,535 bp) region as well as a small single copy (SSC, 15,370 bp) region, is 163,553 bp in total size. The total GC content of this cp genome is 36.0%. TheA. compactumcp genome owns 135 functional genes, that 113 genes are unique, containing eighty protein-coding genes, twenty-nine tRNA (transfer RNA) genes and four rRNA (ribosomal RNA) genes. Codon usage of theA. compactumcp genome is biased toward codons ending with A/T. Total 58 SSR loci and 24 large repeats are detected in theA. compactumcp genome. Relative to three other Zingiberaceae cp genomes, theA. compactumcp genome exhibits an obvious expansion in the IR regions. InA. compactumcp genome, theycf1pseudogene is 2969 bp away from the IRa/SSC border, whereas in other Zingiberaceae species, it is only 4-5 bp away from the IRa/SSC border. Comparative cp genome sequences analysis ofA. compactumwith other Zingiberaceae reveals that the gene order and gene content differ slightly among Zingiberaceae species. The phylogenetic analysis based on 67 protein-coding gene sequences supports the phylogenetic position ofA. compactum. The study has identified unique features of theA. compactumcp genome which would be helpful for us to understand the cp genome evolution and offer useful information for phylogenetics and further studies of this traditional medicinal plant. |
X Demographics
The data shown below were collected from the profiles of 2 X users who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 2 | 100% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 2 | 100% |
Mendeley readers
The data shown below were compiled from readership statistics for 18 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 18 | 100% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Ph. D. Student | 2 | 11% |
| Student > Master | 2 | 11% |
| Student > Bachelor | 1 | 6% |
| Other | 1 | 6% |
| Researcher | 1 | 6% |
| Other | 0 | 0% |
| Unknown | 11 | 61% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 3 | 17% |
| Biochemistry, Genetics and Molecular Biology | 2 | 11% |
| Veterinary Science and Veterinary Medicine | 1 | 6% |
| Psychology | 1 | 6% |
| Unknown | 11 | 61% |
Attention Score in Context
This research output has an Altmetric Attention Score of 2. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 17 February 2018.
All research outputs
#16,053,755
of 25,382,440 outputs
Outputs from Chinese Medicine
#256
of 660 outputs
Outputs of similar age
#259,919
of 455,271 outputs
Outputs of similar age from Chinese Medicine
#7
of 14 outputs
Altmetric has tracked 25,382,440 research outputs across all sources so far. This one is in the 34th percentile – i.e., 34% of other outputs scored the same or lower than it.
So far Altmetric has tracked 660 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 7.0. This one has gotten more attention than average, scoring higher than 58% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 455,271 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 40th percentile – i.e., 40% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 14 others from the same source and published within six weeks on either side of this one. This one is in the 42nd percentile – i.e., 42% of its contemporaries scored the same or lower than it.