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

Journal Article (Journal Article)

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.

Full Text

Duke Authors

Cited Authors

  • Kliver, S; Rayko, M; Komissarov, A; Bakin, E; Zhernakova, D; Prasad, K; Rushworth, C; Baskar, R; Smetanin, D; Schmutz, J; Rokhsar, DS; Mitchell-Olds, T; Grossniklaus, U; Brukhin, V

Published Date

  • March 28, 2018

Published In

Volume / Issue

  • 9 / 4

Start / End Page

  • E185 -

PubMed ID

  • 29597328

Pubmed Central ID

  • PMC5924527

Electronic International Standard Serial Number (EISSN)

  • 2073-4425

International Standard Serial Number (ISSN)

  • 2073-4425

Digital Object Identifier (DOI)

  • 10.3390/genes9040185

Language

  • eng