Arabidopsis halleri Assembly and Gene Annotation
About Arabidopsis halleri
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. The sequenced individual, A. halleri ssp. gemmifera Tada mine genotype (W302), was collected from a site with high contamination by heavy metals in Japan.
Genomic DNA was extracted from plants obtained after five rounds of forced selfing, with heterozygosity reduced to 0.04%. The genome was assembled using ALLPATHS-LG R50599 using three paired end short insert libraries (200 bp, 500 bp, and 800 bp, see Akama et al. 2014) and six long insert mate pair libraries (ranging from 3 kb to 38 kb). The assembly was subsequently improved based on synteny with Arabidopsis lyrata assembly.
Gene annotation was performed with AUGUSTUS v3.0.3 using RNA-seq data from leaves and roots (see Paape et al. 2016). Human readable functional descriptions were generated with AHRD. Out of 32,553 genes, 21,433 were reciprocal best blast hits with Arabidopsis thaliana TAIR10 genes.
Repeated sequences were called with the Repeat Detector, which is part of the Ensembl Genomes repeat feature pipelines. Repeats length: 61005460 - Repeats content: 31.1%
- Conserved but Attenuated Parental Gene Expression in
Allopolyploids: Constitutive Zinc Hyperaccumulation in the
Paape T, Hatakeyama M, Shimizu-Inatsugi R, Cereghetti T, Onda Y, Kenta T, Sese J, Shimizu KK. 2016. Mol Biol Evol. 33(11):2781-2800.
- Genome-wide quantification of homeolog expression ratio revealed
nonstochastic gene regulation in synthetic allopolyploid
Akama S, Shimizu-Inatsugi R, Shimizu KK, Sese J. 2014. Nucleic Acids Res. 42(6):e46.
- Genome assembly and annotation of Arabidopsis halleri, a model for
heavy metal hyperaccumulation and evolutionary
Briskine RV, Paape T, Shimizu-Inatsugi R, Nishiyama T, Akama S, Sese J, Shimizu KK. 2017. Mol Ecol Resour. 17(5):1025-1036.
Picture credit: Arabidopsis halleri subsp. gemmifera, Kinki district, Japan, picture taken by Kentaro K. Shimizu
General information about this species can be found in Wikipedia.
|Assembly||Ahal2.2, INSDC Assembly GCA_900078215.1, Oct 2016|
|Golden Path Length||196,243,198|
|Data source||University of Zurich|
|Non coding genes||670|
|Small non coding genes||657|
|Long non coding genes||13|