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

Publication ,  Journal Article
Kliver, S; Rayko, M; Komissarov, A; Bakin, E; Zhernakova, D; Prasad, K; Rushworth, C; Baskar, R; Smetanin, D; Schmutz, J; Rokhsar, DS ...
Published in: Genes
March 2018

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.

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Published In

Genes

DOI

EISSN

2073-4425

ISSN

2073-4425

Publication Date

March 2018

Volume

9

Issue

4

Start / End Page

E185

Related Subject Headings

  • 3105 Genetics
  • 0604 Genetics
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Kliver, S., Rayko, M., Komissarov, A., Bakin, E., Zhernakova, D., Prasad, K., … Brukhin, V. (2018). Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes. Genes, 9(4), E185. https://doi.org/10.3390/genes9040185
Kliver, Sergei, Mike Rayko, Alexey Komissarov, Evgeny Bakin, Daria Zhernakova, Kasavajhala Prasad, Catherine Rushworth, et al. “Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes.Genes 9, no. 4 (March 2018): E185. https://doi.org/10.3390/genes9040185.
Kliver S, Rayko M, Komissarov A, Bakin E, Zhernakova D, Prasad K, et al. Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes. Genes. 2018 Mar;9(4):E185.
Kliver, Sergei, et al. “Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes.Genes, vol. 9, no. 4, Mar. 2018, p. E185. Epmc, doi:10.3390/genes9040185.
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. Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes. Genes. 2018 Mar;9(4):E185.

Published In

Genes

DOI

EISSN

2073-4425

ISSN

2073-4425

Publication Date

March 2018

Volume

9

Issue

4

Start / End Page

E185

Related Subject Headings

  • 3105 Genetics
  • 0604 Genetics