BrassicaTED - a public database for utilization of miniature transposable elements in Brassica species

Abstract

BackgroundMITE, TRIM and SINEs are miniature form transposable elements (mTEs) that are ubiquitous and dispersed throughout entire plant genomes. Tens of thousands of members cause insertion polymorphism at both the inter- and intra- species level. Therefore, mTEs are valuable targets and resources for development of markers that can be utilized for breeding, genetic diversity and genome evolution studies. Taking advantage of the completely sequenced genomes of Brassica rapa and B. oleracea, characterization of mTEs and building a curated database are prerequisite to extending their utilization for genomics and applied fields in Brassica crops.FindingsWe have developed BrassicaTED as a unique web portal containing detailed characterization information for mTEs of Brassica species. At present, BrassicaTED has datasets for 41 mTE families, including 5894 and 6026 members from 20 MITE families, 1393 and 1639 members from 5 TRIM families, 1270 and 2364 members from 16 SINE families in B. rapa and B. oleracea, respectively. BrassicaTED offers different sections to browse structural and positional characteristics for every mTE family. In addition, we have added data on 289 MITE insertion polymorphisms from a survey of seven Brassica relatives. Genes with internal mTE insertions are shown with detailed gene annotation and microarray-based comparative gene expression data in comparison with their paralogs in the triplicated B. rapa genome. This database also includes a novel tool, K BLAST (Karyotype BLAST), for clear visualization of the locations for each member in the B. rapa and B. oleracea pseudo-genome sequences.ConclusionsBrassicaTED is a newly developed database of information regarding the characteristics and potential utility of mTEs including MITE, TRIM and SINEs in B. rapa and B. oleracea. The database will promote the development of desirable mTE-based markers, which can be utilized for genomics and breeding in Brassica species. BrassicaTED will be a valuable repository for scientists and breeders, promoting efficient research on Brassica species. BrassicaTED can be accessed at http://im-crop.snu.ac.kr/BrassicaTED/index.php.

Maternal components of RNA‐directed DNA methylation are required for seed development in Brassica rapa

“…Transposable elements were annotated in the B. rapa R‐o‐18 genome with RepeatMasker (v. 4‐0.5) using RMBlast and a combined library of exemplar repetitive DNA elements from the following sources: Brassica and Arabidopsis repetitive DNA elements from RepBase (http://www.girinst.org/repbase/) updated through vol17, issue 4; Brassica rapa RepeatModeler‐generated dataset (Cheng et al ., ); Arabidopsis thaliana transposons from TAIR10 (http://ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR10_genome_release/, downloaded 3/27/2017); Brassica MITE, TRIM and SINEs (Murukarthick et al ., ); Brassica rapa MITEs (Chen et al ., ); and Brassica hATs (Nouroz et al ., ). As the RepeatModeler‐generated dataset of repetitive elements included 1037 unclassified elements, 176 of the unclassified elements were manually annotated and used to classify an additional 226 elements based on blastn hits with e‐values <1E‐10.…”

Elucidating the major hidden genomic components of the A, C, and AC genomes and their influence on Brassica evolution

“…oleracea (Bo-1-1) genome sequence was independently analyzed to identify the major REs using the abovementioned approach. Sequences of the individual repeat families for each species were stored in the Brassica TED 48 . In addition, graph-based clustering and characterization of repetitive elements by RepeatExplorer was performed using the 0.1x WGS reads from each B .…”

Miniature Transposable Elements (mTEs): Impacts and Uses in the Brassica Genome

“…TRIM families are distributed throughout the B. rapa and B. oleracea genomes . Though the insertions of five Brassica TRIM families were random, Genome-wide characterization showed that 619 (44 %) and 656 (40 %) of the members of the five Brassica TRIM families reside in or within 2 kb of a gene in the B. rapa and B. oleracea genome, respectively (Yang et al 2007;Murukarthick et al 2014;Table 6.2). Most-TRIM families are present in relatively similar copy numbers between Brassica species but the Cassandra family appears to show high divergence between B. rapa and B. oleracea, based on members found in counterpart paralogous sequences of pseudo-chromosomes (Sampath and Yang 2014a, b).…”