10.5061/DRYAD.GN4HH
Briskine, Roman V.
University of Zurich
Paape, Timothy
University of Zurich
Shimizu-Inatsugi, Rie
University of Zurich
Nishiyama, Tomoaki
Kanazawa University
Akama, Satoru
Biotechnology Research Institute
Sese, Jun
Biotechnology Research Institute
Shimizu, Kentaro K.
Yokohama City University
University of Zurich
Data from: Genome assembly and annotation of Arabidopsis halleri, a model
for heavy metal hyperaccumulation and evolutionary ecology
Dryad
dataset
2016
Arabidopsis halleri
de novo Assembly
heavy metal hyperaccumulator
functional annotation
2016-09-21T14:24:12Z
2016-09-21T14:24:12Z
en
https://doi.org/10.1111/1755-0998.12604
67351530 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
The self-incompatible species Arabidopsis halleri is a close relative of
the self-compatible model plant Arabidopsis thaliana. The broad European
and Asian distribution and heavy metal hyperaccumulation ability make A.
halleri a useful model for ecological genomics studies. We used
long-insert mate-pair libraries to improve the genome assembly of the A.
halleri ssp. gemmifera Tada mine genotype (W302) collected from a site
with high contamination by heavy metals in Japan. After five rounds of
forced selfing, heterozygosity was reduced to 0.04%, which facilitated
subsequent genome assembly. Our assembly now covers 196 Mb or 78% of the
estimated genome size and achieved scaffold N50 length of 712 kb. To
validate assembly and annotation, we used synteny of A. halleri Tada mine
with a previously published high-quality reference assembly of a closely
related species, Arabidopsis lyrata. Further validation of the assembly
quality comes from synteny and phylogenetic analysis of the HEAVY METAL
ATPASE4 (HMA4) and METAL TOLERANCE PROTEIN1 (MTP1) regions using published
sequences from European A. halleri for comparison. Three tandemly
duplicated copies of HMA4, key gene involved in cadmium and zinc
hyperaccumulation, were assembled on a single scaffold. The assembly will
enhance the genomewide studies of A. halleri as well as the allopolyploid
Arabidopsis kamchatica derived from A. lyrata and A. halleri.
Reciprocal best BLAST hits between Arabidopsis halleri and Arabidopsis
thalianaReciprocal best BLAST hits between Arabidopsis halleri ssp.
gemmifera Tada mine and Arabidopsis thaliana
TAIR10.RBH_Ahal_Atha.txt.gzReciprocal best BLAST hits between Arabidopsis
halleri and Arabidopsis lyrataReciprocal best BLAST hits between
Arabidopsis halleri ssp. gemmifera Tada mine and Arabidopsis
lyrata.RBH_Ahal_Alyr.txt.gzRepeatMasker output for the Arabidopsis halleri
assemblyAhal_RepeatMaskerTE.out.gzTransposable elements identified by
RepeatMasker in the Arabidopsis halleri assemblyTransposable elements
identified by RepeatMasker in the Arabidopsis halleri assembly. The output
was converted to GFF format.Ahal_RepeatMaskerTE.gff.gzArabidopsis halleri
assembly with TE maskingArabidopsis halleri assembly with transposable
elements and simple repeats masked by
RepeatMasker.Ahal_masked.fa.gzArabidopsis halleri functional
annotationFunctional annotation for Arabidopsis halleri ssp. gemmifera
Tada mine. The annotation was performed with AUGUSTUS v3.0.3 using RNA-seq
data from leaves and roots.annotation.gff.gzArabidopsis halleri
TranscriptsCoding sequences of all reported transcripts in Arabidopsis
halleritranscripts.fa.gz
135.35E
Inagawa city
Hyogo Prefecture
Japan
Tada mine
34.89N
Osaka Prefecture