Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes
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.
- Authors:
-
- St. Petersburg State Univ., St. Petersburg (Russia); All-Russia Research Institute for Agricultural Microbiology, St.Petersburg (Russia)
- St. Petersburg State Univ., St. Petersburg (Russia)
- Colorado State Univ., Fort Collins, CO (United States)
- Univ. of California, Berkeley, CA (United States)
- Indian Inst. of Technology, Chennai (India)
- Univ. of Zurich, Zurich (Switzerland)
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); HudsonAlpha Inst. of Biotechnology, Huntsville, AL (United States)
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- Duke Univ., Durham, NC (United States)
- St. Petersburg State Univ., St. Petersburg (Russia); Komarov Botanical Institute RAS, St. Petersburg (Russia)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); Univ. of California, Oakland, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1544039
- Alternate Identifier(s):
- OSTI ID: 1615270
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Genes
- Additional Journal Information:
- Journal Volume: 9; Journal Issue: 4; Journal ID: ISSN 2073-4425
- Publisher:
- MDPI
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Genetics & Heredity; Boechera; Brassicaceae; genome; assembly; annotation; apomixis
Citation Formats
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, and Brukhin, Vladimir. Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes. United States: N. p., 2018.
Web. doi:10.3390/genes9040185.
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. United States. https://doi.org/10.3390/genes9040185
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, and Brukhin, Vladimir. Wed .
"Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes". United States. https://doi.org/10.3390/genes9040185. https://www.osti.gov/servlets/purl/1544039.
@article{osti_1544039,
title = {Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes},
author = {Kliver, Sergei and Rayko, Mike and Komissarov, Alexey and Bakin, Evgeny and Zhernakova, Daria and Prasad, Kasavajhala and Rushworth, Catherine and Baskar, R. and Smetanin, Dmitry and Schmutz, Jeremy and Rokhsar, Daniel S. and Mitchell-Olds, Thomas and Grossniklaus, Ueli and Brukhin, Vladimir},
abstractNote = {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.},
doi = {10.3390/genes9040185},
journal = {Genes},
number = 4,
volume = 9,
place = {United States},
year = {Wed Mar 28 00:00:00 EDT 2018},
month = {Wed Mar 28 00:00:00 EDT 2018}
}
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Cited by: 17 works
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Figure 1: Plant (a) and flower (b) of Boechera retrofracta.
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Works referencing / citing this record:
The steps from sexual reproduction to apomixis
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