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X Demographics
Mendeley readers
Attention Score in Context
| Title |
Syntenic gene analysis between Brassica rapa and other Brassicaceae species
|
|---|---|
| Published in |
Frontiers in Plant Science, January 2012
|
| DOI | 10.3389/fpls.2012.00198 |
| Pubmed ID | |
| Authors |
Feng Cheng, Jian Wu, Lu Fang, Xiaowu Wang |
| Abstract |
Chromosomal synteny analysis is important in genome comparison to reveal genomic evolution of related species. Shared synteny describes genomic fragments from different species that originated from an identical ancestor. Syntenic genes are orthologs located in these syntenic fragments, so they often share similar functions. Syntenic gene analysis is very important in Brassicaceae species to share gene annotations and investigate genome evolution. Here we designed and developed a direct and efficient tool, SynOrths, to identify pairwise syntenic genes between genomes of Brassicaceae species. SynOrths determines whether two genes are a conserved syntenic pair based not only on their sequence similarity, but also by the support of homologous flanking genes. Syntenic genes between Arabidopsis thaliana and Brassica rapa, Arabidopsis lyrata and B. rapa, and Thellungiella parvula and B. rapa were then identified using SynOrths. The occurrence of genome triplication in B. rapa was clearly observed, many genes that were evenly distributed in the genomes of A. thaliana, A. lyrata, and T. parvula had three syntenic copies in B. rapa. Additionally, there were many B. rapa genes that had no syntenic orthologs in A. thaliana, but some of these had syntenic orthologs in A. lyrata or T. parvula. Only 5,851 genes in B. rapa had no syntenic counterparts in any of the other three species. These 5,851 genes could have originated after B. rapa diverged from these species. A tool for syntenic gene analysis between species of Brassicaceae was developed, SynOrths, which could be used to accurately identify syntenic genes in differentiated but closely-related genomes. With this tool, we identified syntenic gene sets between B. rapa and each of A. thaliana, A. lyrata, T. parvula. Syntenic gene analysis is important for not only the gene annotation of newly sequenced Brassicaceae genomes by bridging them to model plant A. thaliana, but also the study of genome evolution in these species. |
X Demographics
The data shown below were collected from the profile of 1 X user who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 1 | 100% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 1 | 100% |
Mendeley readers
The data shown below were compiled from readership statistics for 130 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Netherlands | 1 | <1% |
| France | 1 | <1% |
| Pakistan | 1 | <1% |
| Australia | 1 | <1% |
| India | 1 | <1% |
| United States | 1 | <1% |
| Unknown | 124 | 95% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 32 | 25% |
| Student > Ph. D. Student | 27 | 21% |
| Student > Doctoral Student | 10 | 8% |
| Student > Master | 9 | 7% |
| Other | 5 | 4% |
| Other | 15 | 12% |
| Unknown | 32 | 25% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 74 | 57% |
| Biochemistry, Genetics and Molecular Biology | 17 | 13% |
| Computer Science | 3 | 2% |
| Social Sciences | 2 | 2% |
| Environmental Science | 1 | <1% |
| Other | 0 | 0% |
| Unknown | 33 | 25% |
Attention Score in Context
This research output has an Altmetric Attention Score of 1. 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 30 August 2012.
All research outputs
#20,165,369
of 22,675,759 outputs
Outputs from Frontiers in Plant Science
#15,750
of 19,848 outputs
Outputs of similar age
#221,176
of 244,088 outputs
Outputs of similar age from Frontiers in Plant Science
#109
of 195 outputs
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So far Altmetric has tracked 19,848 research outputs from this source. They receive a mean Attention Score of 4.0. This one is in the 1st percentile – i.e., 1% of its peers scored the same or lower than it.
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We're also able to compare this research output to 195 others from the same source and published within six weeks on either side of this one. This one is in the 1st percentile – i.e., 1% of its contemporaries scored the same or lower than it.