| Title |
Revision of Begomovirus taxonomy based on pairwise sequence comparisons
|
|---|---|
| Published in |
Archives of Virology, April 2015
|
| DOI | 10.1007/s00705-015-2398-y |
| Pubmed ID | |
| Authors |
Judith K. Brown, F. Murilo Zerbini, Jesús Navas-Castillo, Enrique Moriones, Roberto Ramos-Sobrinho, José C. F. Silva, Elvira Fiallo-Olivé, Rob W. Briddon, Cecilia Hernández-Zepeda, Ali Idris, V. G. Malathi, Darren P. Martin, Rafael Rivera-Bustamante, Shigenori Ueda, Arvind Varsani |
| Abstract |
Viruses of the genus Begomovirus (family Geminiviridae) are emergent pathogens of crops throughout the tropical and subtropical regions of the world. By virtue of having a small DNA genome that is easily cloned, and due to the recent innovations in cloning and low-cost sequencing, there has been a dramatic increase in the number of available begomovirus genome sequences. Even so, most of the available sequences have been obtained from cultivated plants and are likely a small and phylogenetically unrepresentative sample of begomovirus diversity, a factor constraining taxonomic decisions such as the establishment of operationally useful species demarcation criteria. In addition, problems in assigning new viruses to established species have highlighted shortcomings in the previously recommended mechanism of species demarcation. Based on the analysis of 3,123 full-length begomovirus genome (or DNA-A component) sequences available in public databases as of December 2012, a set of revised guidelines for the classification and nomenclature of begomoviruses are proposed. The guidelines primarily consider a) genus-level biological characteristics and b) results obtained using a standardized classification tool, Sequence Demarcation Tool, which performs pairwise sequence alignments and identity calculations. These guidelines are consistent with the recently published recommendations for the genera Mastrevirus and Curtovirus of the family Geminiviridae. Genome-wide pairwise identities of 91 % and 94 % are proposed as the demarcation threshold for begomoviruses belonging to different species and strains, respectively. Procedures and guidelines are outlined for resolving conflicts that may arise when assigning species and strains to categories wherever the pairwise identity falls on or very near the demarcation threshold value. |
X Demographics
The data shown below were collected from the profiles of 4 X users who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Nigeria | 1 | 25% |
| Indonesia | 1 | 25% |
| Brazil | 1 | 25% |
| Unknown | 1 | 25% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 3 | 75% |
| Scientists | 1 | 25% |
Mendeley readers
The data shown below were compiled from readership statistics for 359 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Brazil | 4 | 1% |
| India | 2 | <1% |
| South Africa | 1 | <1% |
| Costa Rica | 1 | <1% |
| United Kingdom | 1 | <1% |
| Japan | 1 | <1% |
| Unknown | 349 | 97% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Master | 63 | 18% |
| Student > Ph. D. Student | 57 | 16% |
| Researcher | 45 | 13% |
| Student > Bachelor | 25 | 7% |
| Student > Doctoral Student | 20 | 6% |
| Other | 59 | 16% |
| Unknown | 90 | 25% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 163 | 45% |
| Biochemistry, Genetics and Molecular Biology | 63 | 18% |
| Immunology and Microbiology | 7 | 2% |
| Business, Management and Accounting | 4 | 1% |
| Unspecified | 4 | 1% |
| Other | 17 | 5% |
| Unknown | 101 | 28% |
Attention Score in Context
This research output has an Altmetric Attention Score of 4. 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 06 March 2021.
All research outputs
#7,507,658
of 23,758,334 outputs
Outputs from Archives of Virology
#899
of 4,252 outputs
Outputs of similar age
#87,346
of 266,323 outputs
Outputs of similar age from Archives of Virology
#5
of 58 outputs
Altmetric has tracked 23,758,334 research outputs across all sources so far. This one has received more attention than most of these and is in the 68th percentile.
So far Altmetric has tracked 4,252 research outputs from this source. They receive a mean Attention Score of 3.8. This one has done well, scoring higher than 78% 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 266,323 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 66% of its contemporaries.
We're also able to compare this research output to 58 others from the same source and published within six weeks on either side of this one. This one has done particularly well, scoring higher than 93% of its contemporaries.