| |
|
|
| |
|
|
Research  |
|
|
|
| |
| |
funRNA: a fungi-centered genomics platform for genes encoding key components of RNAi
|
|
|
|
|
|
| |
|
 Authours
|
Jaeyoung Choi, Ki-Tae Kim, Jongbum Jeon, Jiayao Wu, Hyeunjeong Song, Fred O Asiegbu,
Yong-Hwan Lee |
| Title |
funRNA: a fungi-centered genomics platform for genes encoding key components of RNAi |
| Journal |
BMC GENOMICS, 2014 (15) ~ |
Abstract
|
Background: RNA interference (RNAi) is involved in genome defense as well as diverse cellular, developmental, and
physiological processes. Key components of RNAi are Argonaute, Dicer, and RNA-dependent RNA polymerase (RdRP),
which have been functionally characterized mainly in model organisms. The key components are believed to exist
throughout eukaryotes; however, there is no systematic platform for archiving and dissecting these important gene
families. In addition, few fungi have been studied to date, limiting our understanding of RNAi in fungi. Here we
present funRNA http://funrna.riceblast.snu.ac.kr/, a fungal kingdom-wide comparative genomics platform for putative
genes encoding Argonaute, Dicer, and RdRP.
Description: To identify and archive genes encoding the abovementioned key components, protein domain profiles
were determined from reference sequences obtained from UniProtKB/SwissProt. The domain profiles were searched
using fungal, metazoan, and plant genomes, as well as bacterial and archaeal genomes. 1,163, 442, and 678 genes
encoding Argonaute, Dicer, and RdRP, respectively, were predicted. Based on the identification results, active site
variation of Argonaute, diversification of Dicer, and sequence analysis of RdRP were discussed in a fungus-oriented
manner. funRNA provides results from diverse bioinformatics programs and job submission forms for BLAST,
BLASTMatrix, and ClustalW. Furthermore, sequence collections created in funRNA are synced with several gene family
analysis portals and databases, offering further analysis opportunities.
Conclusions: funRNA provides identification results from a broad taxonomic range and diverse analysis functions, and
could be used in diverse comparative and evolutionary studies. It could serve as a versatile genomics workbench for
key components of RNAi. |
Link
|
 |
|
|
| |
|
|
|
|
| |
|
|
|
|
