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dc.contributor.author Briskine, Roman V.
dc.contributor.author Paape, Timothy
dc.contributor.author Shimizu-Inatsugi, Rie
dc.contributor.author Nishiyama, Tomoaki
dc.contributor.author Akama, Satoru
dc.contributor.author Sese, Jun
dc.contributor.author Shimizu, Kentaro K.
dc.coverage.spatial Tada mine
dc.coverage.spatial Inagawa city
dc.coverage.spatial Hyogo Prefecture
dc.coverage.spatial Japan
dc.coverage.spatial 34.89N
dc.coverage.spatial 135.35E
dc.date.accessioned 2016-09-22T21:40:24Z
dc.date.available 2016-09-22T21:40:24Z
dc.date.issued 2016-09-27
dc.identifier doi:10.5061/dryad.gn4hh
dc.identifier.citation Briskine RV, Paape T, Shimizu-Inatsugi R, Nishiyama T, Akama S, Sese J, Shimizu KK (2017) Genome assembly and annotation of Arabidopsis halleri, a model for heavy metal hyperaccumulation and evolutionary ecology. Molecular Ecology Resources 17(5): 1025-1036.
dc.identifier.issn 1755-098X
dc.identifier.uri http://hdl.handle.net/10255/dryad.121203
dc.description 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.
dc.relation.haspart doi:10.5061/dryad.gn4hh/2
dc.relation.haspart doi:10.5061/dryad.gn4hh/3
dc.relation.haspart doi:10.5061/dryad.gn4hh/4
dc.relation.haspart doi:10.5061/dryad.gn4hh/5
dc.relation.haspart doi:10.5061/dryad.gn4hh/6
dc.relation.haspart doi:10.5061/dryad.gn4hh/1
dc.relation.haspart doi:10.5061/dryad.gn4hh/7
dc.relation.isreferencedby doi:10.1111/1755-0998.12604
dc.relation.isreferencedby PMID:27671113
dc.subject de novo assembly
dc.subject functional annotation
dc.subject heavy metal hyperaccumulator
dc.title Data from: Genome assembly and annotation of Arabidopsis halleri, a model for heavy metal hyperaccumulation and evolutionary ecology
dc.type Article
dwc.ScientificName Arabidopsis halleri
dc.contributor.correspondingAuthor Shimizu, Kentaro
prism.publicationName Molecular Ecology Resources
dryad.dansTransferDate 2018-05-10T06:30:11.452+0000
dryad.dansEditIRI https://easy.dans.knaw.nl/sword2/container/9bb8b1f5-5ff2-447e-9c8a-0db4a5d56163
dryad.dansArchiveDate 2018-05-10T08:02:03.833+0000

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Title Reciprocal best BLAST hits between Arabidopsis halleri and Arabidopsis thaliana
Downloaded 50 times
Description Reciprocal best BLAST hits between Arabidopsis halleri ssp. gemmifera Tada mine and Arabidopsis thaliana TAIR10.
Download RBH_Ahal_Atha.txt.gz (106.3 Kb)
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Title Reciprocal best BLAST hits between Arabidopsis halleri and Arabidopsis lyrata
Downloaded 17 times
Description Reciprocal best BLAST hits between Arabidopsis halleri ssp. gemmifera Tada mine and Arabidopsis lyrata.
Download RBH_Ahal_Alyr.txt.gz (113.2 Kb)
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Title RepeatMasker output for the Arabidopsis halleri assembly
Downloaded 21 times
Download Ahal_RepeatMaskerTE.out.gz (2.437 Mb)
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Title Transposable elements identified by RepeatMasker in the Arabidopsis halleri assembly
Downloaded 19 times
Description Transposable elements identified by RepeatMasker in the Arabidopsis halleri assembly. The output was converted to GFF format.
Download Ahal_RepeatMaskerTE.gff.gz (1.413 Mb)
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Title Arabidopsis halleri assembly with TE masking
Downloaded 25 times
Description Arabidopsis halleri assembly with transposable elements and simple repeats masked by RepeatMasker.
Download Ahal_masked.fa.gz (42.41 Mb)
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Title Arabidopsis halleri functional annotation
Downloaded 55 times
Description Functional 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.
Download annotation.gff.gz (8.257 Mb)
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Title Arabidopsis halleri Transcripts
Downloaded 33 times
Description Coding sequences of all reported transcripts in Arabidopsis halleri
Download transcripts.fa.gz (12.60 Mb)
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