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Genome assembly and annotation of Arabidopsis halleri , a model for heavy metal hyperaccumulation and evolutionary ecology
Author(s) -
Briskine Roman V.,
Paape Timothy,
ShimizuInatsugi Rie,
Nishiyama Tomoaki,
Akama Satoru,
Sese Jun,
Shimizu Kentaro K.
Publication year - 2017
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/1755-0998.12604
Subject(s) - biology , synteny , arabidopsis , genome , sequence assembly , phylogenetic tree , evolutionary biology , genetics , gene , gene expression , transcriptome , mutant
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 .