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

Sergei Kliver, Mike Rayko, Alexey Komissarov, Evgeny Bakin, Daria Zhernakova, Kasavajhala Prasad, Catherine Rushworth, R. Baskar, Dmitry Smetanin, Jeremy Schmutz, Daniel S. Rokhsar, Thomas Mitchell-Olds, Ueli Grossniklaus, Vladimir Brukhin

Research output: Contribution to journalArticleResearchpeer-review

5 Citations (Scopus)

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.

Original languageEnglish
Article number185
Number of pages16
JournalGenes
Volume9
Issue number4
DOIs
StatePublished - 1 Apr 2018

Keywords

  • Boechera
  • Brassicaceae
  • genome
  • assembly
  • annotation
  • apomixis
  • MULTIPLE SEQUENCE ALIGNMENT
  • ABERRANT CHROMOSOMES
  • APOMICTIC BOECHERA
  • SEXUAL DIPLOIDS
  • BRASSICACEAE
  • SUBSTITUTIONS
  • REPRODUCTION
  • PHYLOGENIES
  • GENETICS
  • DATABASE
  • Apomixis
  • Annotation
  • Genome
  • Assembly

Scopus subject areas

  • Genetics(clinical)
  • Genetics

Cite this

Kliver, Sergei ; Rayko, Mike ; Komissarov, Alexey ; Bakin, Evgeny ; Zhernakova, Daria ; Prasad, Kasavajhala ; Rushworth, Catherine ; Baskar, R. ; Smetanin, Dmitry ; Schmutz, Jeremy ; Rokhsar, Daniel S. ; Mitchell-Olds, Thomas ; Grossniklaus, Ueli ; Brukhin, Vladimir. / Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes. In: Genes. 2018 ; Vol. 9, No. 4.
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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.",
keywords = "Boechera, Brassicaceae, genome, assembly, annotation, apomixis, MULTIPLE SEQUENCE ALIGNMENT, ABERRANT CHROMOSOMES, APOMICTIC BOECHERA, SEXUAL DIPLOIDS, BRASSICACEAE, SUBSTITUTIONS, REPRODUCTION, PHYLOGENIES, GENETICS, DATABASE, Apomixis, Annotation, Genome, Assembly",
author = "Sergei Kliver and Mike Rayko and Alexey Komissarov and Evgeny Bakin and Daria Zhernakova and Kasavajhala Prasad and Catherine Rushworth and R. Baskar and Dmitry Smetanin and Jeremy Schmutz and Rokhsar, {Daniel S.} and Thomas Mitchell-Olds and Ueli Grossniklaus and Vladimir Brukhin",
year = "2018",
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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 2018, 'Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes', Genes, vol. 9, no. 4, 185. https://doi.org/10.3390/genes9040185, https://doi.org/10.3390/genes9040185

Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes. / Kliver, Sergei; Rayko, Mike; Komissarov, Alexey; Bakin, Evgeny; Zhernakova, Daria; Prasad, Kasavajhala; Rushworth, Catherine; Baskar, R.; Smetanin, Dmitry; Schmutz, Jeremy; Rokhsar, Daniel S.; Mitchell-Olds, Thomas; Grossniklaus, Ueli; Brukhin, Vladimir.

In: Genes, Vol. 9, No. 4, 185, 01.04.2018.

Research output: Contribution to journalArticleResearchpeer-review

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T1 - Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes

AU - Kliver, Sergei

AU - Rayko, Mike

AU - Komissarov, Alexey

AU - Bakin, Evgeny

AU - Zhernakova, Daria

AU - Prasad, Kasavajhala

AU - Rushworth, Catherine

AU - Baskar, R.

AU - Smetanin, Dmitry

AU - Schmutz, Jeremy

AU - Rokhsar, Daniel S.

AU - Mitchell-Olds, Thomas

AU - Grossniklaus, Ueli

AU - Brukhin, Vladimir

PY - 2018/4/1

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N2 - 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.

AB - 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.

KW - Boechera

KW - Brassicaceae

KW - genome

KW - assembly

KW - annotation

KW - apomixis

KW - MULTIPLE SEQUENCE ALIGNMENT

KW - ABERRANT CHROMOSOMES

KW - APOMICTIC BOECHERA

KW - SEXUAL DIPLOIDS

KW - BRASSICACEAE

KW - SUBSTITUTIONS

KW - REPRODUCTION

KW - PHYLOGENIES

KW - GENETICS

KW - DATABASE

KW - Apomixis

KW - Annotation

KW - Genome

KW - Assembly

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U2 - 10.3390/genes9040185

DO - 10.3390/genes9040185

M3 - статья

VL - 9

JO - Genes

JF - Genes

SN - 2073-4425

IS - 4

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