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Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes

Type of publication Peer-reviewed
Publikationsform Original article (peer-reviewed)
Author Kliver Sergei, Rayko Mike, Komissarov Alexey, Bakin Evgeny, Zhernakova Daria, Prasad Kasavajhala, Rushworth Catherine, Baskar R., Smetanin Dmitry, Schmutz Jeremy, Rokhsar Daniel, Mitchell-Olds Thomas, Grossniklaus Ueli, Brukhin Vladimir,
Project Sequencing, assembly, and annotation of the highly heterozygous genome of the apomictic plant Boechera divaricarpa
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Original article (peer-reviewed)

Journal Genes
Volume (Issue) 9(4)
Page(s) 185 - 185
Title of proceedings Genes
DOI 10.3390/genes9040185

Open Access

Type of Open Access Publisher (Gold Open Access)


Closely related to the model plant Arabidopsis thaliana, the genus Boechera is known to contain both sexual and apomictic species or accessions. Boechera retrofracta is a diploid sexually reproducing species and is thought to be an ancestral parent species of apomictic species. Here we report the de novo assembly of the B. retrofracta genome using short Illumina and Roche reads from 1 paired-end and 3 mate pair libraries. The distribution of 23-mers from the paired end library has indicated a low level of heterozygosity and the presence of detectable duplications and triplications. The genome size was estimated to be equal 227 Mb. N50 of the assembled scaffolds was 2.3 Mb. Using a hybrid approach that combines homology-based and de novo methods 27,048 protein-coding genes were predicted. Also repeats, transfer RNA (tRNA) and ribosomal RNA (rRNA) genes were annotated. Finally, genes of B. retrofracta and 6 other Brassicaceae species were used for phylogenetic tree reconstruction. In addition, we explored the histidine exonuclease APOLLO locus, related to apomixis in Boechera, and proposed model of its evolution through the series of duplications. An assembled genome of B. retrofracta will help in the challenging assembly of the highly heterozygous genomes of hybrid apomictic species.