Abstract
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.
Highlights
Among over the 370 genera belonging to the family Brassicaceae (Cruciferae), only the genusBoechera shows asexual reproduction by seeds [1,2,3,4]
It was shown that the APOLLO locus has several alleles with apomixis-associated polymorphisms
In this study we decided to take a closer look to this locus in our assembly and other Brassicaceae species in this study
Summary
Boechera shows asexual reproduction by seeds [1,2,3,4]. Apomixis is defined as asexual reproduction through seeds that results in progeny identical to the maternal plant. The Boechera genus includes 110 sexual and apomictic species, widely distributed in North America. Plants from the Boechera genus are represented by biannual and perennial herbs with a chromosome base number of n = 7 [8,9]. Apomixis in the Boechera genus is of special interest because it can occur at the diploid level, which is very rare [1,2,3,4,5,6,7,8]. The phylogenetic proximity of Boechera to the model plant
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