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X Demographics
Mendeley readers
Attention Score in Context
| Title |
New Insights on Eggplant/Tomato/Pepper Synteny and Identification of Eggplant and Pepper Orthologous QTL
|
|---|---|
| Published in |
Frontiers in Plant Science, July 2016
|
| DOI | 10.3389/fpls.2016.01031 |
| Pubmed ID | |
| Authors |
Riccardo Rinaldi, Allen Van Deynze, Ezio Portis, Giuseppe L. Rotino, Laura Toppino, Theresa Hill, Hamid Ashrafi, Lorenzo Barchi, Sergio Lanteri |
| Abstract |
Eggplant, pepper, and tomato are the most exploited berry-producing vegetables within the Solanaceae family. Their genomes differ in size, but each has 12 chromosomes which have undergone rearrangements causing a redistribution of loci. The genome sequences of all three species are available but differ in coverage, assembly quality and percentage of anchorage. Determining their syntenic relationship and QTL orthology will contribute to exploit genomic resources and genetic data for key agronomic traits. The syntenic analysis between tomato and pepper based on the alignment of 34,727 tomato CDS to the pepper genome sequence, identified 19,734 unique hits. The resulting synteny map confirmed the 14 inversions and 10 translocations previously documented, but also highlighted 3 new translocations and 4 major new inversions. Furthermore, each of the 12 chromosomes exhibited a number of rearrangements involving small regions of 0.5-0.7 Mbp. Due to high fragmentation of the publicly available eggplant genome sequence, physical localization of most eggplant QTL was not possible, thus, we compared the organization of the eggplant genetic map with the genome sequence of both tomato and pepper. The eggplant/tomato syntenic map confirmed all the 10 translocations but only 9 of the 14 known inversions; on the other hand, a newly detected inversion was recognized while another one was not confirmed. The eggplant/pepper syntenic map confirmed 10 translocations and 8 inversions already detected and suggested a putative new translocation. In order to perform the assessment of eggplant and pepper QTL orthology, the eggplant and pepper sequence-based markers located in their respective genetic map were aligned onto the pepper genome. GBrowse in pepper was used as reference platform for QTL positioning. A set of 151 pepper QTL were located as well as 212 eggplant QTL, including 76 major QTL (PVE ≥ 10%) affecting key agronomic traits. Most were confirmed to cluster in orthologous chromosomal regions. Our results highlight that the availability of genome sequences for an increasing number of crop species and the development of "ultra-dense" physical maps provide new and key tools for detailed syntenic and orthology studies between related plant species. |
X Demographics
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 3 | 100% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 3 | 100% |
Mendeley readers
The data shown below were compiled from readership statistics for 59 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 59 | 100% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 18 | 31% |
| Student > Ph. D. Student | 15 | 25% |
| Student > Master | 7 | 12% |
| Professor > Associate Professor | 3 | 5% |
| Student > Bachelor | 2 | 3% |
| Other | 6 | 10% |
| Unknown | 8 | 14% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 32 | 54% |
| Biochemistry, Genetics and Molecular Biology | 11 | 19% |
| Nursing and Health Professions | 2 | 3% |
| Business, Management and Accounting | 1 | 2% |
| Arts and Humanities | 1 | 2% |
| Other | 2 | 3% |
| Unknown | 10 | 17% |
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 18 July 2016.
All research outputs
#15,380,162
of 22,880,691 outputs
Outputs from Frontiers in Plant Science
#10,900
of 20,270 outputs
Outputs of similar age
#233,711
of 363,150 outputs
Outputs of similar age from Frontiers in Plant Science
#261
of 537 outputs
Altmetric has tracked 22,880,691 research outputs across all sources so far. This one is in the 22nd percentile – i.e., 22% of other outputs scored the same or lower than it.
So far Altmetric has tracked 20,270 research outputs from this source. They receive a mean Attention Score of 4.0. This one is in the 40th percentile – i.e., 40% of its peers scored the same or lower than it.
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We're also able to compare this research output to 537 others from the same source and published within six weeks on either side of this one. This one is in the 44th percentile – i.e., 44% of its contemporaries scored the same or lower than it.